Sequence
atgc intronic sequence ATGC exonic sequence...atcttcttcgtaaatttgttttgcatttgaatctttacgatctcccttcccccttttcctgctagggtcttgacaaatttctagatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTTTGCAGCTTTG
Basic information
species | Glycine max |
transcript | GLYMA11G38110.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 1
---atcttcttcgtaaatttgttttgcatttgaatctttacgatctccc---ttcccccttttcctgcta-gggtcttgacaaatttctagatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTTTGCAGCTTTG
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gtggaatttcccgcatgcatgtcatatattatgcttgacagaatgtagtatgttagtaatttgcttcttacgccttttgtcacatgtgtacttggtc-------cagGCAACGATTGGCATTGACTTTCTGTCAAAAACAATGTATCTAGAAGACCGAACTGTACGTTTACAACTCTG
upper sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 1
----atcttcttcgtaaatttgttttgcatttgaatctttacgatctcccttcccccttttcctgctagggtcttgacaaatttctagatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTTTGCAGCTTTG
|| | || | || | ||| | | | || | | ||| | || || | || |||| | | | ||| |||| ||||| || || || | || |||||||||||||| |||||||||||||||||||||||||| ||
tcttattatgatca-agatcgatgatgc-taagcactgttgcttctttgctttcttagttagtcattaagcctttatttgtgttctctctgactct--ctgcagCCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATG
upper sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------------------------------atcttctt--cgtaa--atttgttttgcatttgaatctttacgatctcccttcccccttttcct--gctagggtcttgacaaatttctagatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTTTGCAGCTTTG
||| | || |||| | | | | | | |||| || | ||| | | ||| | | | | ||| | | || | || ||||| || ||||| ||||| || ||||||||||||||||||||||| ||| | || |||||| | || || ||
gttggatcattttcttctatcccatctcgatcaaaattaattttgatccattgtctgtgagatccacgatcctgttgctgtaatgaatggatcagattcagaattgctagaaactcatagcattgtgttcattggatcaaattctgatat-tagttatggtgtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
upper sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 1
atcttcttcgtaaatttgtt-ttgcatttgaatctttacgatctcc------cttcccccttttcctgctagggtcttgacaaatttctagatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTTTGCAGCTTTG
| ||| || | || || | ||| | | | | |||| | || | | |||| | |||| | | |||| | |||||||||||||| ||||||||||| || |||||||||||||||||||||||||| |||||| ||||||| ||
-tagatcatgtagatacaatgctgaatgtaaatttcttttagttgtagtaatcttcacaaaatttatacattagtctc-ataaatctttgtttcat-----tcacagGCTACTATTGGAATTGACTTCTTATCGAAAACAATGTACCTTGAAGATCGAACTGTTCGTCTGCAGCTATG
upper sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
-atcttcttcgtaaatttgttttgcatttgaatctttacgatctcccttcccccttttcct--gctagggtcttgacaaatttctagatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTTTGCAGCTTTG
| ||| ||| ||| | | | | | || || ||| | | || ||| | | | || | | |||| |||||||| ||||| ||||| || ||||| ||||| ||||||||||| ||||||||| ||||||||||||||||
aaaaagaaaaaaaaaattggtttatctaggtaatctgtctattggagttaaaattttaaattagttacattctcttgatactcct---ttttggtaattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
upper sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 2
--atcttcttcgtaaatttgttttgcatttgaatctttacgatctcccttcccccttttcctgctagggtcttgacaaatttctagatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTTTGCAGCTTTG
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tgttcatgtgcgaaaatctgatgcacgaaaatattgttcaatttttcaaaacttcgaagtgttctgtggttatggtga-taaccaaatt-ttatgtttgcagGCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcccccttttcctgctagggtcttgacaaatttctagatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTTTGCAGCTTTG
tcttgac putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcttcttcgtaaatttgttttgcatttgaatctttacgatctcccttcccccttttcctgctagggtcttgacaaatttctagatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTTTGCAGCTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- cttcttc
- - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgaca