IRESite_Id:287 summary record describing characteristics of NDST1 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `287`	Version: `4`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2007-04-20 00:00:00`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `nonexisting_chimera_of_GenBank_record_and_tested_IRES_fragment`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `NDST1`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
145279230

The mRNA/+RNA description:

Hypothetical mRNA sequence of NDST1 assembled in silico by two-step multiple sequence alignment of selected
GenBank EST and mRNA sequences.

The mRNA/+RNA sequence represented in the +DNA notation:

GGTGCACGCC CGGGACCGGC GGCCGCGCGG CCACCCGCGC CGCTTCCCCC TGGCGTCCCG GCCGAGGCAG CATCCCAGCC TTTACCCTGT GGGCCCAACG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGAGGAGTGT GAGGAGCGGC ATGCGGCGCC CCCTGGCTGG TTCGGTGTCT TTTGACCTGC TGTTGACTGC TCCCAGGGGG CCCTGACGCC CTGGGGCACT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TTTGCTCTGC ACAGGACCAC GCTGGGGTTT GCCATGGTGA CATAAAGGGG TGTAGAGGAA GGAAGGAGCA AGACCAGCCT GTAGACTGTG CCCCTGGCTG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GGCAAAAGGG CCAGGGGCCC GGAGCCTTCC CTCCACTGCC CTCGAACGCC TCACTTCCTA AGTCTCTGCA TTTCTCAGTC AGTGGACAGC TTTTGGGACT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTTGTGTGAG GACTTTGGGG GACCAGGCCA GGCTGGGCCT CTGCTGATTG AGATCTTGGG ATCCAGAATG CCTGCCCTGG CGTGCCTCCG GAGGCTGTGT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CGGCACCTGT CCCCACAGGC TGTCCTGTTC CTGCTGTTCG TCTTCTGCCT GTTCAGCGTT TTTGTCTCTG CCTACTACCT ATATGGTTGG AACCGGGGCC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TTGAGCCCTC GGCAGATGCT TCCGAGTCTG ACTGTGGGGA CCCGCCACCT GTCGCCCCTA GCCGCCTCCT GCCAATCAAG CCCGTGCAGG CGGTTGCCCC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TTCCCGAACA GACCCACTGG TGCTGGTATT TGTGGAGAGC CTTTATTCAC AGCTGGGCCA GGAGGTGGTG GCAATCCTGG AATCCAGTCG CTTCAAATAC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CGGACAGAGA TTGCACCGGG CAAGGGGGAC ATGCCCACAC TCACAGACAA GGGCCGTGGC CGCTTCGCCC TCATCATCTA CGAGAACATC CTCAAGTATG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TCAACCTGGA TGCCTGGAAC CGGGAGCTGC TGGACAAGTA CTGTGTGGCC TACGGCGTGG GCATCATTGG ATTCTTCAAG GCCAATGAGA ACAGCCTGCT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GAGTGCACAG CTCAAAGGCT TCCCTCTCTT CCTGCATTCG AACCTGGGCT TGAAAGACTG CAGCATCAAC CCCAAGTCAC CACTGCTCTA TGTGACACGG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CCCAGTGAGG TAGAGAAAGG CGTGCTGCCC GGAGAGGATT GGACTGTGTT CCAGTCCAAC CATTCTACCT ACGAACCAGT GCTGTTGGCC AAGACACGCT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CCTCCGAATC CATCCCACAC CTGGGTGCTG ATGCTGGCCT GCATGCTGCG CTGCACGCTA CTGTGGTCCA GGACCTGGGT CTCCACGATG GCATCCAGCG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TGTGCTCTTT GGCAACAACC TCAACTTTTG GCTGCATAAG CTTGTCTTCG TGGATGCTGT GGCCTTCCTC ACGGGGAAGC GCCTCTCACT GCCTTTGGAC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CGATACATCC TGGTGGATAT TGATGACATT TTTGTGGGCA AGGAGGGCAC ACGCATGAAG GTGGAGGATG TGAAGGCCCT GTTTGATACA CAGAATGAAC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TCCGCACACA TATTCCAAAC TTCACCTTCA ACCTGGGCTA CTCAGGGAAA TTCTTCCACA CAGGTACGGA TGCTGAGGAT GCTGGCGACG ATCTGCTGTT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GTCCTATGTG AAAGAGTTCT GGTGGTTCCC CCACATGTGG AGCCATATGC AACCCCACCT CTTCCACAAC CAATCTGTGC TGGCAGAGCA GATGGCCCTG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AACAAGAAGT TCGCTGTCGA GCACGGCATC CCCACAGATA TGGGCTATGC GGTGGCGCCC CACCACTCCG GTGTGTACCC TGTGCACGTG CAGCTGTATG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AGGCCTGGAA GCAAGTGTGG GGCATCCGTG TGACCAGCAC AGAGGAGTAC CCACATCTGA AGCCGGCCCG GTACCGCCGT GGCTTTATCC ACAATGGCAT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CATGGTCCTC CCTCGGCAGA CCTGTGGCCT CTTTACACAC ACCATCTTCT ACAACGAGTA CCCTGGAGGC TCCAGTGAGC TGGACAAGAT CATCAATGGG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GGCGAGCTCT TCCTCACTGT GCTCCTCAAT CCTATCAGCA TCTTCATGAC ACACTTATCC AACTATGGAA ATGACCGCCT GGGACTATAC ACCTTCAAGC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ACCTGGTGCG CTTCCTGCAC TCCTGGACCA ACCTGAGGCT GCAGACTCTG CCCCCCGTGC AGCTGGCCCA GAAGTACTTT CAGATCTTTT CTGAGGAGAA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GGACCCGCTT TGGCAGGATC CCTGTGAGGA CAAACGCCAC AAGGACATCT GGTCTAAGGA GAAGACATGT GACCGCTTCC CAAAGCTTCT TATCATTGGC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CCCCAGAAAA CAGGCACCAC GGCCCTCTAC CTGTTCCTGG GCATGCACCC GGACCTCAGC AGCAACTACC CCAGCTCCGA GACCTTCGAG GAGATCCAGT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTTTTAACGG CCACAACTAT CACAAAGGCA TCGACTGGTA CATGGAGTTC TTCCCTATTC CCTCCAACAC CACCTCGGAC TTCTACTTTG AGAAAAGTGC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CAACTACTTT GATTCAGAAG TGGCACCACG GCGGGCAGCT GCACTGTTGC CCAAGGCCAA GATCCTCAGC ATCCTCATCA ACCCAGCCGA CCGGGCTTAT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TCCTGGTACC AGCACCAGCG AGCCCATGAT GACCCAGTGG CCCTAAAGTA CACCTTTCAT GAGGTGATCA CAGCTGGCCC TGATGCATCC TCAAAGCTGC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GTGCCCTCCA GAACCGGTGC CTGGTCCCAG GCTGGTATGC CACTCATATT GAACGCTGGC TCAGCGCCTT TCATGCCAAC CAGATCCTGG TCTTGGATGG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CAAACTGCTG CGAACAGAAC CTGCCAAAGT CATGGACACA GTGCAGAAAT TCCTTGGGGT GACCAGCACT GTCGACTACC ATAAAACCTT GGCGTTTGAT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CCAAAGAAGG GATTTTGGTG CCAACTGCTT GAAGGAGGAA AAACCAAGTG TCTGGGAAAA AGCAAGGGAC GGAAATATCC AGAGATGGAC TTGGATTCCC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GAGCCTTCCT AAAGGATTAC TTCCGGGACC ACAACATTGA GCTCTCTAAG CTGCTGTATA AGATGGGCCA GACACTGCCC ACCTGGCTGC GGGAAGACCT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CCAGAACACC AGGTAGCCTT GGCCACCACA GCCAGCCAGA ACGCTTGTGT TCGCAGGGAT GTCCTGCCTC ACACTGAGCC AGACTGACCT GCCGAGAAGG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AAGCTGGGCC CAGCCAGCCA AAAGCGACGA GCAATACTCT GCTGAGGCCC ACAGGGGCCG GAAGCCCAGG CAGGTCTGCA AGCGCCTCAG AGCATCCACC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GCTGGATGCA TGGCCTGTGG GACCTCTGTG GTACCAGAGG TCCATTCCGT TCCTTCGCAG CCTCCCTGCC TGGGGAGAGC ACTTCCTGTT GTTGGAAGGT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CATTTCCTGG TAGGAGGAGT CCTGGAGGCT CTCTCCTGTC CCTCACTGTG TCCTACCGTT CCTGTCCTGT CCTTTGTCAC CCCCCCTCCC GCTCCATCAG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GATGTCCCCT CAGTATTAGC TGCCATAGTT CTTCTGTCCT CCAGACAGTA AAGGGGAAGA GCGCAGCTGG GCCTTTCGCC CAACCAGGGA GAAAGACTGG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

GCATGTCCCT GAGGGTTTTG AGCCAGGCCC TGCCAGGGTT TAGCTAGGCA CCCAGATGCA CTCATTAGAC TGAATGTGAG GGTGACCATC TTGAGAGGAC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ATACGACTCT GTATTTGGGT TATTATTATC ACATCTCATC TCCTCTTTGG GAAAAGACTC TCTGGTCCCT ATTGTATCCA CCTAGTAGTG CTCATGGTCT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CTCGTAGGCC CTGGGCCACT GCCATGCCAC TGGGCCCAGA GACGTGGGCC TTGGCCCCGT CCTGCTCACC TGGATGTGAC ATGTGGTGTT TCCTGTGGTA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

AAGGCTGAGG CGAGTCAGGA GTCTGCCAGT GTTCATAGTC CCGTGTACAT AGATTGTTTC ACAGCTGCCG CCTCGGCCCA GCAGACATGG CAGTCAGCAA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

GCAGTGCTGT CCGCTGCTTT GCCTAGCAAC CTGTGGCCGA GGGTCCCCAG AGACCCCCTA ACCTCCCAAA TACTAAGAAG CTAAAGTATT TTAATATTTT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GTGTTTTTTT TTTTTCTTGG TGCCAGAGTT TATACCCTGG GTGCTGGGGT CGCACTGTGT TTTATATATA TATATATATA TATGAAATGT GTATATATAT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

ATTATATATT TTTTTTGGTT GGGTTTGTTT TTAATTCAGT CATATACAAT GATGGCAAGC CCGAGCCTCA AAGAATGTCG TATCTTAATG CTAGAGAATG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

AGGTGGAAAG GAAGGTGAGT GTCTATGAGC ACCCAGGCCT CAGGGCGAAG TCTTGAAGGG TCCTTCTTCC CTCTTCTGCA GAGGGACCAG AGATGCTAAG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

ATGGAAAGGA AGACCAGCTC TCCCAAAATA GTATGGCTTT ACAAAGCCTA GTGGCCGTGG GGTGTTTGGG CCACAGGGAA AGGCTGGCCC GGGGTGGGAC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

ACCTGGGGCC CTGAGCTGGC CTCTCCCTCC CCTGTCACAT GGTGCTAGGT TGGGGTCTGC TTTGGAGTGG GGTGCCCACA GGGACCCACA GAACTGTCTC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

CAGTCCCTGA AGACACAGGG TCTTTGGCTG GTTTCTGTTT GGATTCTGTT TCTGTCCCCC TTTTAACAAT GTGAAGTGAC TGAGGTTGGA TTTCCTCTTC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CTGCTACCCC AAGCCCCCAC ATCTCTTTAA CTGCCAGTCC AGTGTCCACC AGCCATTTGT TCTGACATCC TGGCCATGCA AGGGTCCCAA GACGGGCACA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

AAGTGGGTCC AGGCATGGGA GGTGGCCTTG GTCAATGTCA CAGAGCTGTT GGAAGCAGTG CCAAGAGCTA AATTCAGGCC CCTGATTCTG AGCCCCGTGC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

TCTTCCAGTA CCACACTGCC TCTGAGCCTG CCTTCGGGAC CCTACTGTGT TCCAGGTCCC GTCTGTCCCT CAGTCACATA GCTGTGGTCA TTCCAGGACA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TGGGGACAAA CCACTCTTTC CCAGCCAGGT GCCTTTGAGC CTTCCCTTCC AAGACCTGCA CTTTTCCCGC TGTGTTCTCT TGTTTCCAGA GTCCATCCAT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

CTTACTAGCT GGGGTCGTCT TCATTATGAG CTATTCCTTC CTGGAGTTCT CCACTGTGGT GGAGAGTGTG GGATGCTCAG AGGGACCTGC GTGCATGGTT 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

TTGGTGTGCA GAGAGCCATG TCACATCATG TTTCTCACTG GGGTCTTGGA ACCTGTGGAT CCCAGTCCCT ATGTGATATG CTCAAATGCC CTGTCAACAA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

GCTAGAACCA GACTCAGGGT TAGGTCAGTG TGCATGCCCT TAGCCACACT TCCCACCTGT CAGTGAGGAT GGCTCCTATA TTCTGAAAGC TACTCTGAGA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CCCTGTGAGA GCTGAGTTAG ATGGTTGGAG TGGCCTTTAG ATAGCATGCA GCTCTGTTAG TCTCTGCTTC TGGTCTCCAT TGAAAGCAAG CAGGTTTGAG 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

ACCCTGGCAG AGCAGGGGAG TGGTTCTCTC TGGTCCATTT CCCTCTAAGA CCCTGGAAAC TGCTGCTGTG TCCCTTTCAG TGCTGGGCCT AGAGGCTGCC 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

ACAAGTTGCA GATGTGGGGT CTTGGGAAGT AGATACGTTC ATCTTAGTAT CTCTCAATGA CAATGTCCAC TGATTGACTG GAAACGTTTG GAAAAACACA 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

AAAACAAGTT GGAAGGAAAT TACTTCTGTT GTTCAGGCCA CACCCTGTCC CTTCTTCAGT CTCTACCAAC AGCGTTTGCC TTATGGGTGC AGCTCACCGG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

CAGCTGCCTC ATTCATTCCA GGTTCTAGAG CTTTCTATGG GGCGGGTACC TCGGTGCGCA TAGGGAATGA GGACGAAGCT AAAATGGACC TTTCAAACCC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CGATGTATGA GCAATGGGTG CTTGTGAGTC TGCTCATTTC CAGAGGAGAA GTCCTGGCCT GCCCCACCCT AGAGCCCCCC AGGTGTGTGA GTGGCAAGAG 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

CAAGCTCAGA ACCGTCTCAG CGCTGGGCTG TGACTGCCAG CCACCCTTCA TCTAGACTGA AGGAGGTTAG CATTTGCCAG TGTGTTTTCT CTCGATATTC 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ATGTACGTGT ATTTTAAAAG TAAGTTGCAG TATCATGAGA CTATTTATCC CTAGTGTTGC CCTAAGAGGT AGGGCCTTTT ACCAGACCAG CCAGTGCCAC 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

AGCCAAGACA GTAGTCCTGT CCCACTAACA GCCATTGTCT AGTCTGTACC TAAAGTTGTC TCCCAGCCCC CATTCTACCC CATTATTTTA GTATTGGTAT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TGGATCCAAT CAGGGCAAGA ACATTGTATG TTATTAAAAA GTTTCTTTGA AAGCTAAAAA GTTTTCCCTC TGCCCAACTC ATT
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381

Credibility of mRNA sequence:

only_fragment_published_or_from_author_and_the_rest_is_a_guess

The organism containing this mRNA with IRES segment in its genome:

Mus musculus C57BL/6

A promoter reported in cDNA corresponding to IRES sequence:
no (not convincing) The total number of notable open-reading frames (ORFs):
1

Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:

Summary of experiments studying integrity of the in vivo transcripts in a particular host:

Integrity (uniformity) of mRNA tested using Northern-blot:
homogeneous_population_of_molecules_confirmed

Integrity (uniformity) of mRNA tested using RNase protection:
not_tested

Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested

Integrity (uniformity) of mRNA tested using primer extension :
not_tested

Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested

Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested

Integrity (uniformity) of mRNA tested using RNAi:
not_tested

Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested

Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
not_tested

Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested

Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested

The organism used:

Cricetulus griseus CHO-K1 (ATCC CCL-61)

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
NDST1

The description of the protein encoded in this ORF:
N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
no

The alternative forms of this protein occur by the alternative initiation of translation:

not tested

The ORF absolute position (the base range includes START and STOP codons or their equivalents):

468-3116

Remarks:

Hypothetical mRNA sequence of NDST1 assembled in silico by two-step multiple sequence alignment polished by
manual editing. First, EST sequences matching the cloned 5'-UTR region from mouse skin, brain and testis (and
deposited to GenBank under GI:21780279, 418bp) were aligned and resulting 5'-UTR region consensus sequence
partly overlapping to ORF region was created. The ORF overlapping sequence was used to find NDST1 protein
records, and their mRNA sequences were aligned to the consensus sequence created previously. The final
consensus sequence is this hypothetical mRNA. Please note several EST were longer at the 5'-end while having different
alignment in largers blocks (could be different exons). Therefore, the actually cloned sequence by Grobe was only
extended at the 5'-end using the sequence from highly similar sequences.

For consensus sequence of 5'-UTR were used records GI# 76220104, 76277345, 76226443, 76212202, 76223509,
76212796, 76205756, 76230649, 27165322, 21780279 (the one published by Grobe et al., 2002), 50077330,
27178085, 26312028, 26068161, 17112028, 17092705, 27181493, 5493626, 76201866, 76202831, 76201865, 26370099,
6632294. For consensus sequence of ORF and 3'-UTR were used records GI:145279230, GI:4322250, GI:41946075,
GI:50925369.

The sequence deposited in IRESite is the final consensus sequence but was trimmed at the 3'-end from poly(A)
sequence.

Citations:

Grobe K., Esko J. D. (2002) Regulated translation of heparan sulfate N-acetylglucosamine N-deacetylase/n-sulfotransferase isozymes by structured 5'-untranslated regions and internal ribosome entry sites. J. Biol. Chem. 277(34):30699-30706

IRESs:

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `NDST1`

The IRES absolute position (the range includes START and STOP codons or their equivalents):

48-467

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

The sequence of IRES region aligned to its secondary structure (if available):

CCCTGGCGTC CCGGCCGAGG CAGCATCCCA GCCTTTACCC TGTGGGCCCA ACGTGAGGAG TGTGAGGAGC GGCATGCGGC GCCCCCTGGC TGGTTCGGTG 
^48        ^58        ^68        ^78        ^88        ^98        ^108       ^118       ^128       ^138       

TCTTTTGACC TGCTGTTGAC TGCTCCCAGG GGGCCCTGAC GCCCTGGGGC ACTTTTGCTC TGCACAGGAC CACGCTGGGG TTTGCCATGG TGACATAAAG 
^148       ^158       ^168       ^178       ^188       ^198       ^208       ^218       ^228       ^238       

GGGTGTAGAG GAAGGAAGGA GCAAGACCAG CCTGTAGACT GTGCCCCTGG CTGGGCAAAA GGGCCAGGGG CCCGGAGCCT TCCCTCCACT GCCCTCGAAC 
^248       ^258       ^268       ^278       ^288       ^298       ^308       ^318       ^328       ^338       

GCCTCACTTC CTAAGTCTCT GCATTTCTCA GTCAGTGGAC AGCTTTTGGG ACTCTTGTGT GAGGACTTTG GGGGACCAGG CCAGGCTGGG CCTCTGCTGA 
^348       ^358       ^368       ^378       ^388       ^398       ^408       ^418       ^428       ^438       

TTGAGATCTT GGGATCCAGA
^448       ^458

Citations:

Last change to the database: 2019-03-18 09:32:49 GMT+1