A database of hypoxia responsive genes in fishes
 
  Hypoxia-Response element (HRE) mining in the upstream

  • A 3000 nt (-2900,100) upstream sequences of the gene start site (reported on genomic sequence) have been taken for analysis and prediction of functional HRE
  • Kimura (2001) reported functional HREs (5'-RCGTG-3') in different mammalian genes, which consisted consensus HAS located 7-9 nt downstream
  • Kajimura (2006) reported functional HRE 5'-(A|G)CGTG-3' with HAS (CAGGT), which was located 15 nt downstream in the upstream of IGFBP1 gene in zebrafish
  • This HRE analysis module mines all canonical HREs, including forward and reverse orientation in the upstream of a gene. Further, this module predicts all possible functional HREs using HRE [5'-RCGTG-3'] sequence and adjacent HAS [5'-CA(G|C)(A|G)(T|G|C)-3'] consensus sequences located 7-15 nt downstream

  Gene list     Select the strand     

A 3000 nt long upstream sequences were used to compute HRE distibution among the available 12 orthologous 'igfbp1' genes
S.No.GeneSpeciesLocationHRE sequence
1igfbp1Astyanax mexicanus291 - 321
5'-ACGTGCCAGCGCTTGAACGGACTTGTATTA-3'
370 - 400
5'-ACGTGTGAACCCGGTCTGTGTTCTCCTCTC-3'
459 - 489
5'-GCGTGCGCGCGCGAAAAAAGAGAAAGGGGG-3'
513 - 543
5'-ACGTGTGAACCGTCATGTCCCGCGTCTATT-3'
2541 - 2571
5'-ACGTGTGGTAAAATCTGAGTGGTTCACAAT-3'
2653 - 2683
5'-GCGTGTGGTCTTAAGTGTAGCTCGTGGTGA-3'
2764 - 2794
5'-ACGTGTATTGCGTGCGCGGCGCGCTCTCCA-3'
2773 - 2803
5'-GCGTGCGCGGCGCGCTCTCCAATCAGCGCC-3'
2igfbp1Austrofundulus limnaeus190 - 220
5'-ACGTGTTCAATACTTATTTTACCCGCTGAA-3'
1249 - 1279
5'-GCGTGTGGTCATATTTTGTTTTTTCCAAGG-3'
3igfbp1Boleophthalmus pectinirostris290 - 320
3'-GCGTGTTTTCAGCTCACCGATCGACCGCGG-5'
1631 - 1661
3'-GCGTGTCCTTTGCATTTGATCCATCGCTGG-5'
2412 - 2442
3'-ACGTGAAACTTACATTTTTTTGAGAATCCA-5'
4igfbp1Carassius auratus1088 - 1118
3'-GCGTGCACTAGCACTGTGGTACGTGACCTC-5'
1108 - 1138
3'-ACGTGACCTCACTCAGGTCACGACGGGACC-5'
1459 - 1489
3'-GCGTGGAGTTTCTCTACGTGTCACGTGATA-5'
1474 - 1504
3'-ACGTGTCACGTGATAGTTGTCCGTTCACTC-5'
1481 - 1511
3'-ACGTGATAGTTGTCCGTTCACTCGTGTGTG-5'
1605 - 1635
3'-ACGTGTAAATGTTGTCAGACTACGAAGGAT-5'
2173 - 2203
3'-ACGTGGTCTTTCAGAAATCATTCTAATAGG-5'
5igfbp1Danio rerio75 - 105
3'-ACGTGGAGTTCCTCACTGTCTTTGCGCTCT-5'
317 - 347
3'-GCGTGAAAAGCGTGTGTTTACTACCCGACA-5'
326 - 356
3'-GCGTGTGTTTACTACCCGACAAGTACCTAA-5'
1173 - 1203
3'-GCGTGCACTCGCCCTGTGGTACGTGACCTC-5'
1193 - 1223
3'-ACGTGACCTCACTCAGGTCAGGACGGCACC-5'
1516 - 1546
3'-GCGTGGAGAGTTTCTCTGCGCGTCACGTGA-5'
1540 - 1570
3'-ACGTGATCAGGTTGTCCGTTCGCGCGCGTG-5'
1565 - 1595
3'-GCGTGTGGGAACGCGAGTATCTGCTGACGG-5'
6igfbp1Fundulus heteroclitus232 - 262
3'-ACGTGCGCGGAGCCCCGCTCACAAGGTCGG-5'
733 - 763
3'-GCGTGACGTACAAGCCCACACACACACACA-5'
7igfbp1Paralichthys olivaceus223 - 253
3'-ACGTGCGTAGATCCAGGTTCACAAGGTCTG-5'
468 - 498
3'-GCGTGTGTGTTGTCAAACACTTATTCAGTT-5'
8igfbp1Poecilia formosa2476 - 2506
5'-GCGTGATGCGATGAACCTTCACCAGCAAGC-3'
2632 - 2662
5'-ACGTGGAGGTTATTTAATATTTACTGATTT-3'
9igfbp1Poecilia mexicana2461 - 2491
5'-GCGTGATGCGATGAACCTTCACCAGCAAGC-3'
2630 - 2660
5'-ACGTGGAGGTTATTTAATATTTACTGATTT-3'
10igfbp1Poecilia reticulata217 - 247
3'-GCGTGACGTGCACAGATCCATGCTTACAAG-5'
222 - 252
3'-ACGTGCACAGATCCATGCTTACAAGGTCTG-5'
1158 - 1188
3'-ACGTGTTTGTCCCAAAAAGAATAAAGAAGG-5'
11igfbp1Takifugu rubripes719 - 749
3'-GCGTGAAGACTGTTATTCTAAGAGTCATAA-5'
1885 - 1915
3'-GCGTGTTTTAAAGAAAGACGGGTGGGAGGA-5'
2222 - 2252
3'-GCGTGGGTCAGCGGGCTGCTGCCCGCGCTG-5'
2252 - 2282
3'-GCGTGGACGGAGGAGATGCTGCCCAGATTG-5'
2317 - 2347
3'-GCGTGCCAGGCTGGCGGAACGAACCACTGA-5'
12igfbp1Xiphophorus couchianus215 - 245
3'-ACGTGCACAGATCCATGCTTACAAGGTCTC-5'



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