Sequence
atgc intronic sequence ATGC exonic sequencegtaagttacagtgtctcttgaaatgccggtggatgcacattttcactttctagctgcagtctggctggattttgatgcgtcaatcacaaatgttaaattgaaaattttagttttgtaaatttgagtgtagtttatttattcttggataaaatggaccaagttacttgtttcagGGAATAGAAAAGAAGACTGCCAAGTTGAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTAGTAGGTACTGCAGTTGCAAACC
Basic information
species | Glycine max |
transcript | GLYMA02G39040.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 9
gtaagttacagtgtctcttgaaatgccggtggatgcacattttcactttctagctgcagtctggctggattttgatgcgtcaatcacaaatgttaaattgaaaattttagttttgtaaatttgagtgtagtttatttattcttggataaaatggaccaagttacttgtttcagGGAATAGAAAAGAAGACTGCCAAGTTGAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTAGTAGGTACTGCAGTTGCAAACC
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-------------------------------------------------------tcaatattgttatggaa-gatgtatctgttccagctgttagagtagacatt---gttttac---ttcca--------cattgtttcctgga--aactaactggaattattt-tcttagGGCATTGAGAAAAAGCATGCAAAGCTGAAGGGTAATGAAAAGGCTGTTGTTGCACGGCATGAAGTTGGTCATGCCGTTGTGGGAACTGCTGTAGCAAACC
upper sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagttacagtgtctcttgaaatgccggtggatgcacattttcactttctagctgcagtctggctggattttgatgcgtcaatcacaaatgttaaattgaaaatttta--gttttgtaaatttgagtgtagtttatttattcttggataaaatggaccaagttacttgtttcagGGAATAGAAAAGAAGACTGCCAAGTTGAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTAGTAGGTACTGCAGTTGCAAACC
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--------------------------------------------------------------------------------------------gtatctctataacctcgctgttttattgatt---acgtaaggcaattgtcaaaatgtgttttcttacaaag-acctgtttcagGGCATAGAGAAGAAATCTGCAAGATTAAAAGGCAATGAGAAGGCAGTGGTCGCAAGGCATGAAGCTGGGCATGCAGTGGTTGGTACCGCTGTTGCAAATC
upper sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagttacagtgtctcttgaaatgccggtggatgcacattttcactttctagctgcagtctggctggattttgatgcgtcaatcacaaatgttaaattgaaaattttagttttgtaaatttgagtgtagtttat-ttattcttggataaaatggaccaagttacttgtttcagGGAATAGAAAAGAAGACTGCCAAGTTGAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTAGTAGGTACTGCAGTTGCAAACC
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----------------------------------------------------------------------------------------------gtattgtc--ttattctttctgagtctctatcgtacctctcatcagaatttgtttccttacattgcatcgtttgcttcagGGCATAGAGAAGAAAACAGCTAGGTTAAAAGGTAGTGAGAAAGCTGTGGTTGCAAGGCATGAAGCTGGGCATGCTGTTGTTGGTACAGCTGTTGCAAGTC
upper sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 9
gtaagttacagtgtctcttgaaatgccggtggatgcacattttcactttctagctgcagtctggctggattttgatgcgtcaatcacaaatgttaaattgaaaattttagttttgtaaatttgagtgtagtttatttattcttggataaaatggaccaagttacttgtttcagGGAATAGAAAAGAAGACTGCCAAGTTGAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTAGTAGGTACTGCAGTTGCAAACC
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--------------------------------------------------------------agacaagttttaagtcat-agtgaagctttcttaat--acaattatcatgtcttgaatccttgttagactgact-------gcatagc-tcaaccaactgtcttgttatagGGCATAGAAAAGAAGACCACCAAGTTGCAGGGAAGTGAGAAGGCTGTTGTTGCACGGCATGAAGCTGGTCATGCAGTAGTGGGAACTGCTGTTGCTAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgagtgtagtttatttattcttggataaaatggaccaagttacttgtttcagGGAATAGAAAAGAAGACTGCCAAGTTGAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTAGTAGGTACTGCAGTTGCAAACC
cttgtttc CT-rich tract
tttatttattcttgga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttacagtgtctcttgaaatgccggtggatgcacattttcactttctagctgcagtctggctggattttgatgcgtcaatcacaaatgttaaattgaaaattttagttttgtaaatttgagtgtagtttatttattcttggataaaatggaccaagttacttgtttcagGGAATAGAAAAGAAGACTGCCAAGTTGAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTAGTAGGTACTGCAGTTGCAAACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG