HRGFish

A resource on hypoxia responsive genes in fish

Hypoxia-Response elemnts (HRE) mining in the upstream

A 3000 nt (-2900,100) upstream sequences of the gene start site have been taken for promoter analysis and hypothetical identification 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 sequence, located upstream, were used to computes HRE distibution among the available 12 orthologous 'igfbp1' genes

S.No.	Gene	Species	Location	HRE sequence
1	igfbp1	Astyanax mexicanus	291 - 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'
2	igfbp1	Austrofundulus limnaeus	190 - 220	5'-ACGTGTTCAATACTTATTTTACCCGCTGAA-3'
2	igfbp1	Austrofundulus limnaeus	1249 - 1279	5'-GCGTGTGGTCATATTTTGTTTTTTCCAAGG-3'
3	igfbp1	Boleophthalmus pectinirostris	290 - 320	3'-GCGTGTTTTCAGCTCACCGATCGACCGCGG-5'
			1631 - 1661	3'-GCGTGTCCTTTGCATTTGATCCATCGCTGG-5'
			2412 - 2442	3'-ACGTGAAACTTACATTTTTTTGAGAATCCA-5'
4	igfbp1	Carassius auratus	1088 - 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'
5	igfbp1	Danio rerio	75 - 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'
6	igfbp1	Fundulus heteroclitus	232 - 262	3'-ACGTGCGCGGAGCCCCGCTCACAAGGTCGG-5'
6	igfbp1	Fundulus heteroclitus	733 - 763	3'-GCGTGACGTACAAGCCCACACACACACACA-5'
7	igfbp1	Paralichthys olivaceus	223 - 253	3'-ACGTGCGTAGATCCAGGTTCACAAGGTCTG-5'
7	igfbp1	Paralichthys olivaceus	468 - 498	3'-GCGTGTGTGTTGTCAAACACTTATTCAGTT-5'
8	igfbp1	Poecilia formosa	2476 - 2506	5'-GCGTGATGCGATGAACCTTCACCAGCAAGC-3'
8	igfbp1	Poecilia formosa	2632 - 2662	5'-ACGTGGAGGTTATTTAATATTTACTGATTT-3'
9	igfbp1	Poecilia mexicana	2461 - 2491	5'-GCGTGATGCGATGAACCTTCACCAGCAAGC-3'
9	igfbp1	Poecilia mexicana	2630 - 2660	5'-ACGTGGAGGTTATTTAATATTTACTGATTT-3'
10	igfbp1	Poecilia reticulata	217 - 247	3'-GCGTGACGTGCACAGATCCATGCTTACAAG-5'
			222 - 252	3'-ACGTGCACAGATCCATGCTTACAAGGTCTG-5'
			1158 - 1188	3'-ACGTGTTTGTCCCAAAAAGAATAAAGAAGG-5'
11	igfbp1	Takifugu rubripes	719 - 749	3'-GCGTGAAGACTGTTATTCTAAGAGTCATAA-5'
			1885 - 1915	3'-GCGTGTTTTAAAGAAAGACGGGTGGGAGGA-5'
			2222 - 2252	3'-GCGTGGGTCAGCGGGCTGCTGCCCGCGCTG-5'
			2252 - 2282	3'-GCGTGGACGGAGGAGATGCTGCCCAGATTG-5'
			2317 - 2347	3'-GCGTGCCAGGCTGGCGGAACGAACCACTGA-5'
12	igfbp1	Xiphophorus couchianus	215 - 245	3'-ACGTGCACAGATCCATGCTTACAAGGTCTC-5'

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