Sequence
atgc intronic sequence ATGC exonic sequence...aattatcttcttcgtaaatttgttttgcacaatgtttccatctcccttcccccttttcctgctagggtcttgacaaatttcttgatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTCTGCAGCTTTG
Basic information
species | Glycine max |
transcript | GLYMA18G02040.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 1
---aattatcttcttcgtaaatttgttttgcacaatgtttccatctcccttcccccttttcctgctagggtcttgacaaatttcttgatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTCTGCAGCTTTG
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tcttattatgatcaagatcgatg-atgctaagcactgttgcttctttgctttcttagttagtcattaagcctttatttgtgttctctctgactct--ctgcagCCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATG
upper sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------------------------------aattatcttcttcgtaaatttgttttgcacaatgtttccat---ctcccttcccccttttcct--gctagggtcttgacaaatttcttgatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTCTGCAGCTTTG
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gttggatcattttcttctatcccatctcgatcaaaattaattttgatccattgtctgtgagatccacgatcctgttgctgtaatgaatggatcagattcagaattgctagaaactcatagcattgtgttcattggatcaaattctgatattagttatggt-gtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
upper sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 1
aattatcttcttcgtaaatttgttttgcacaatgtttccatctccct-tcccccttttcctgctagggtcttgaca--aatttcttga----tcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTCTGCAGCTTTG
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-------tagatcatgtagatacaatgctgaatgtaaatttcttttagttgtagtaatcttcacaaaatttatacattagtctcataaatctttgtttcattcacagGCTACTATTGGAATTGACTTCTTATCGAAAACAATGTACCTTGAAGATCGAACTGTTCGTCTGCAGCTATG
upper sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
--aattatcttcttcgtaaatttgttttgcacaatgtttccatctcccttcccccttttcct--gctagggtcttgacaaatttcttgatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTCTGCAGCTTTG
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aaaaagaaaaaaaaaattggtttatctag-gtaatctgtctattggagttaaaattttaaattagttacattctcttgatactcctttttggt---aattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
upper sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 2
aattatcttcttcgtaaatttgttttgcacaa----tgtttccatctcccttcccccttttcctgctagggtcttgacaaatttcttgatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTCTGCAGCTTTG
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--tgttcatgtgcgaaaatctgatgcacgaaaatattgttcaatttttcaaaacttcgaagtgttctgtggttatggtga--taaccaaattttatgtttgcagGCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcccccttttcctgctagggtcttgacaaatttcttgatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTCTGCAGCTTTG
atcaaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattatcttcttcgtaaatttgttttgcacaatgtttccatctcccttcccccttttcctgctagggtcttgacaaatttcttgatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTCTGCAGCTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - cttcttc
- - - - - - - - - - - - -tgcacaa
- - - - - - - - - - - - - - - - tgtttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgaca