Sequence
atgc intronic sequence ATGC exonic sequencegtacaatattcattttactcaaaaaaattgtacactctatggaatagagatggaacaagatttgttagaggaagactattgtttattttaattaatttcaattgtgctgcagCATAATGCAGAACCTGAAGCTGTTGATCTTTTGATGGAG
Basic information
species | Glycine max |
transcript | GLYMA06G44340.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 7
---------------------------gtacaatatt--cattttactcaaaaaaattgtacactctatggaatagagatgg--aacaagatttgttagaggaagactat-tgtttattttaattaatttcaatt-gtgctgcagCATAATGCAGAACCTGAAGCTGTTGATCTTTTGATGGAG
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gttggttgacttgattcttatcagagattttggttttggtatttaatttgatgctctgattgatgccacttagtagctgtagctgttgttatttgtttgacataattaatgcattaatggtgctttattgtaatttgtaatgcagCATAATGCTGAACCTGAAGCAGTTGATCTTCTGATGGAG
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g48640.2 (Oryza sativa), 3'ss of exon 7
gtacaatattcattttactcaaaaaaattgtacactctatggaatagagatggaacaagatttgttagaggaagactattgtttattttaattaatttcaattgtgctgcagCATAATGCAGAACCTGAAGCTGTTGATCTTTTGATGGAG
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----aaaagtcaa---agcgacaactattgcgggatggaggtagtagccaataaacaactagtatcaatggatgg--actgatgatattgatta---ttatttatattgcagCATAATGCTGAACCTGAAGCTGTGGATCTTCTAATGGAG
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os09g15750.1 (Oryza sativa), 3'ss of exon 7
-------------------------------gtacaatattcattttact-caaaaaaattgt-acactctatggaat------agagatggaacaagatttgttagaggaagactattgtttattttaat--taatt-tcaattgtgctgcagCATAATGCAGAACCTGAAGCTGTTGATCTTTTGATGGAG
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gtcaattttgagtagagtccatgggtgtcattttttaaaaaaatttcattgcaaatgtcttgttacacttggtgtaatgcattaaatattagcaaataaactactagtgctcgatcaatggatggactgatactgattatcatttatattgcagCATAATGCTGAACCTGAAGCTGTGGATCTCCTAATGGAG
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacaatattcattttactcaaaaaaattgtacactctatggaatagagatggaacaagatttgttagaggaagactattgtttattt-taattaatttcaattgtgc--tgcagCATAATGCAGAACCTGAAGCTGTTGATCTTTTGATGGAG-------------------------------------------------------------
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-----------------------------gtgaattcct--aaactaatagggcttgagattagcacctctgcgatt--tatttatttctaaacgatttcatttactccttgcagCATAATGCAGAAACCGAAGCTGTTGATCTTTTAATGGATGTTGAGGATCTTGATCTCTTACTTGAGCATGTAGACAAAACAAATTTCAAGAGGACATGCA
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------gtacaatattcattttactcaaaaaaattgtac-actctatggaatagagatgg-aacaagatttgtta-gag----gaagactattgtttattttaattaattt-----caattgtgctgcagCATAATGCAGAACCTGAAGCTGTTGATCTTTTGATGGAG
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gtgtgttaatttcaaaagttttgattgggttcacatctgtgtaacaaagaacgaaaatattggtgtctgttatggcttttgtaactgcatttgtcatgagattagaaaacttttattttttgtttctgatatttatacatttgcattgcagCACAATGCTGAACCAGAAGCTGTTGATCTTCTGATGGAG
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S414_22V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------gtacaatattcattttactcaaaa---aaattgtacactctatggaatagagatggaacaagatttgttagagga---agactattgtttattttaattaatttcaattgtgctgcagCATAATGCAGAACCTGAAGCTGTTGATCTTTTGATGGAG
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gtaaattatgggattagcagttgcacttcggtgtttgaaatagttgatttttccagcctctgatttgcaggagcagtgcatgccccgctgttttagtttgtttggataagttacgttaatgtttgacaaggtgttggtgattttctctgcagCATAATGCAGAACCTGAAGCAGTGGATCTTCTAATGGAG
upper sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ26022 (Selaginella moellendorffii), 3'ss of exon 6
gtacaatattcattttactcaaaaaaattgtacactctatggaatagagatggaacaagatt-tgttagaggaagactattgtttattttaattaatttca--attgtgct-gcagCATAATGCAGAACCTGAAGCTGTTGATCTTTTGATGGAG
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-----gtatgt-ctttgtttatagttcttttgctgattttatcatgcagTCGGAGGAAGAGTACATCAGCAGCTTGATGG-ATTTAGTAAAGCAAATTGTACCATTCCACTTGCAGCACAATGCAGAACCTGAAGCTGTAGATCTGCTAA-----Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|193712443|gb|FK650166.1|FK650166EST: TGGAACTTGTGCAACAAATTGTTGCTTTTCACATGAAG CATAATGCAGAACCTGAAGCTGTTGATCTTTTGATGGAG
genomic: TGGAACTTGTGCAACAAATTGTTGCTTTTCACATGAAGgtacaatatt ... tgtgctgcagCATAATGCAGAACCTGAAGCTGTTGATCTTTTGATGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatttgttagaggaagactattgtttattttaattaatttcaattgtgctgcagCATAATGCAGAACCTGAAGCTGTTGATCTTTTGATGGAG
aattaat putative branch site (score: 3)
aagactattgtttatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaatattcattttactcaaaaaaattgtacactctatggaatagagatggaacaagatttgttagaggaagactattgtttattttaattaatttcaattgtgctgcagCATAATGCAGAACCTGAAGCTGTTGATCTTTTGATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA