Sequence
atgc intronic sequence ATGC exonic sequence...acatcttatgatattgatttagactctttttttgtttgtttttttttcacttttgtttattgtcttgttttgatcctagtataaatcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG
Basic information
species | Glycine max |
transcript | GLYMA12G02450.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G068913_T01 (Zea mays), 3'ss of exon 5
acatc-ttatgatattgatttagactctttttttgtttgtttttttttcacttttgtttattgtctt-gttttgatcctagtataaatcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG
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gtattattctcttgctgctttgctctgtatccaaattatcaatatcatcgatttatcctgtggacaaagatgtagttcttattcaatcgttcaattcatcagGTTGTAAACATGGAATGGGGCAATTTCTGGTCATCACATTTGCCAAGAACTCCTTATGACATCTCCCTTGATGATGAGACGCAAAATCGCAATGATCAG
upper sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G20040.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------acatcttatgatattgatttagactctttttttgtttgtttttttttcac----ttttgtttatt-gtcttgttttgatcctagtataaatcttctgtt------tattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG
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gtaataactattaagaatcgttacatagttcatccttagaaaccagccatcaaagtttagattccacaggattcaatttaaaagacttgattttttcttctttatgatactttgttattttgtgttagGTGGTCAATATGGAGTGGGGAAACTTTTGGTCATCTCGTCTGCCAAGAACTTCATATGACCTTGAGTTGGATGCAGAGAGTATGAATTCAAATGACATG
upper sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 5
acatcttatgatattgatttagactctttttttgtttgtttttttttcacttttgtttattgtcttgttttgatcctagtataaatcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG
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--gtactaaga-atcattgcatggtctatttttagaaaccagctttagacccaaaagaaacat----gtttaagattgattc---cctcttatgtttcagGTGGTAAATATGGAGTGGGGAAATTTTTGGTCCTCTCATTTGCCTAGAACTTCGTATGACATTGACTTGGATGCAGAGAGTTCAAATGCAAATGATATG
upper sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0061g00040.t01 (Vitis vinifera), 3'ss of exon 5
---acatcttatgatattg-atttagactctttttttgtttgtttttttttcacttttgttt-attgtcttgttt-tgatcctagtataa---atcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG
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gtatcctttcttgattttctagtcatacattacctaacactgcatttttgagaataaagactgattcttctatttattatttgacttcatgtcatcttccattcgttagGTTGTCAACATGGAATGGGGAAATTTCTGGTCATCACATTTGCCAAGAACATCTTACGATATTGATTTAGATGGTGATAGTCCTAATCCAAATGATCAG
upper sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S401_23V6.1 (Physcomitrella patens), 3'ss of exon 4
acatcttatgatattgatttagactctttttttgtttgtttttttttcacttttgtttattgtcttgttttgatcctagtataaatcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG
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actgctctcgtgtaggatatgacttggaatttcgggtgggtttgaatattgaccacgtacccttacataacaagtgatatatggttcctgaccttggcagGTGATCAATATGGAGTGGGGAAACTTTTGGTCATCACATTTGCCTCGGACCTATGTGGATGAGTTATTGGATAGCGAGAGCCTCCATCCAGGAGAATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcacttttgtttattgtcttgttttgatcctagtataaatcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG
ttttgat putative branch site (score: 4)
tcttctgttt putative PPT
ttttgtttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatcttatgatattgatttagactctttttttgtttgtttttttttcacttttgtttattgtcttgttttgatcctagtataaatcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG
- - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg