Sequence
atgc intronic sequence ATGC exonic sequence...ttgtgattaaaccgtacttaagatgtaacttcaacaagaaaacttcatacttatttgatcatttttaattttaattgtgaatttgtgatgaaactagtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA
Basic information
species | Glycine max |
transcript | GLYMA09G02960.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g13190.1 (Oryza sativa), 3'ss of exon 8
ttgtgattaaaccgtacttaagatgtaacttcaacaagaaaacttcatacttatttgatcatttttaattttaattgtgaatttgtg-atgaaactagtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA
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-aatgctttagttgcactagtatttttctgtactcatttattcataacaattgtgtcatttccattatttgtggtgatcaacttatatactgtctttgtagGTTGAAAAAATATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAG
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 10
--ttgtgattaaaccgtacttaagatgtaacttcaacaagaaaacttcatacttatttgatcatttttaattttaattgtgaatttgtgatgaaactagtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA
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tcaccaagttctacagcatttttttatgatttcctgtattggctgtgcactctcattcaaccacata-acttttgctaacttcattacaatgtccata-cagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------ttgtgattaaaccgtacttaagatgtaacttcaacaagaaaacttcatacttatttgatcattttt----aattttaattg---tgaatttgtgatgaaactagt------agGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA
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gtgtgtctgtgttagttttttttcgcttatgttttcatgctggtgattgtattttttct-ctctaagattgtagacat-ttcgattttgttttgcagGCTATAGCTGCCATGGCCTGGGGGACAGATTCTTGTCCAAAGGTTGAGAAGATTTTTGGTCCTGGGAACCAGTATGTCACAGCTGCTAAGATGATTCTTC--
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 10
ttgtgattaaaccgtacttaagatgta--acttcaacaagaaaacttcatacttatttga--tcatttttaattttaattgtgaatttgtgatgaaactagtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA
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ctttgagtta-cttcatcaaagatgtagtattttaattagttttgcttggctgcatcagaaatgacatccagttctaagtgt-atttagtcat--aatttgcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catacttatttgatcatttttaattttaattgtgaatttgtgatgaaactagtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA
ttttaat putative branch site (score: 3)
ttatttgatcattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtgattaaaccgtacttaagatgtaacttcaacaagaaaacttcatacttatttgatcatttttaattttaattgtgaatttgtgatgaaactagtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgatg