Sequence
atgc intronic sequence ATGC exonic sequencegtatagtatctctatttgattacacttgcccttgcaatgtaataatacatgcgcttttgttccttgcacagAATGCCCAGCAAATCCATGGTCCTTTTCTTGTAGTTGTTCCATTGTCCACTTTATCAAATTGGGCCAAAGAATTCAGGAAGTGGCTTCCTGATATGAATA
Basic information
species | Glycine max |
transcript | GLYMA02G45000.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 10
-----------gtatagtatctctatttgattacacttgcccttgcaa---tgtaataatacatgcgcttttgttccttg-cacagAATGCCCAGCAAATCCATGGTCCTTTTCTTGTAGTTGTTCCATTGTCCACTTTATCAAATTGGGCCAAAGAATTCAGGAAGTGGCTTCCTGATATGAATA
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gtaattatttctcattgtattttcttgtcatcattatgatgaatgaaattgtcttttaatattgatatctgatttatttgtcgcagAATGCTCAAGAAATCAATGGTCCATTTCTTGTAGTTGTGCCACTGTCAACATTGTCGAACTGGGCAAAAGAATTTCGGAAGTGGCTGCCCAACATGAATG
upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 11
lower sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 12
-----------------------------------------------------------gtatagtatctctatttgattacacttgcccttgca-atgtaataatacatgcgcttttgttccttgcacagAATGCCCAGCAAATCCATGGTCCTTTTCTTGTAGTTGTTCCATTGTCCACTTTATCAAATTGGGCCAAAGAATTCAGGAAGTGGCTTCCTGATATGAATA
| | | ||| | | | | || || || || | | | || ||| || | |||||| |||| ||||| | ||||||||||||||| ||||| || ||||| || || | |||||||| |||||||| || ||||||||||| | |||||||
gtgaaaatctttttcttttcaagtgagcgttcaagtttgctcatgatttggaaatcttgttctcttttcttagcattacttttcatgagctaacatatctcttcttttatttcttttcttttttcttgcagAATACCCAACAAATTCCTGGTCCTTTTCTTGTTGTTGTGCCTTTGTCAACACTAGCTAATTGGGCTAAAGAATTTAGAAAGTGGCTTCCCGGCATGAATA
upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------------------------------------------------------gtat-agtatctctatttgattacacttgcccttgcaatgtaataatacatgcg--cttttgttccttgc-acagAATGCCCAGCAAATCCATGGTCCTTTTCTTGTAGTTGTTCCATTGTCCACTTTATCAAATTGGGCCAAAGAATTCAGGAAGTGGCTTCCTGATATGAATA
||| | ||| || ||| || | || ||||| | | ||||| || | | || || || ||||||||| || ||||| |||| || |||||||| ||||| ||||| || ||||||||||| ||||| |||||||||| ||||||||||||||| |||||
gtaagcatctagtagttattattagtagtattattattgcttttgtgtttattatcatttattgttattgttgttgtcattattattattattattacttttttcttgtagtt--ccttgtagacttataatccaaggaaacattcatttgttcttacagAATGCTCAACAAATATATGGACCATTTCTTGTTGTTGTACCATTATCGACTTTATCAAACTGGGCAAAAGAATTCAAGAAGTGGCTTCCTGACTTGAATG
upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S317_10V6.1 (Physcomitrella patens), 3'ss of exon 12
-----------------------------gtatagtatctctat-ttgattacact-tgcccttgcaatgtaataatacatgcgcttttgttccttgcacagAATGCCCAGCAAATCCATGGTCCTTTTCTTGTAGTTGTTCCATTGTCCACTTTATCAAATTGGGCCAAAGAATTCAGGAAGTGGCTTCCTGATATGAATA
| ||| || | |||| | ||| | | | | | | || ||| || | ||| | | |||| || ||||| | ||| |||||||| |||||||| ||| | ||||| | | ||||||||||||||||| |||||||| | ||||||||||||
gatccccacaaaaaaaccgtttttatcttgcataataaacatgcgttgacttaactctatctctttccttttctgggttgtgggctgtttcttgttgta--gTATGCTCAACAAATTCCTGGACCTTTTCTGGTAGTTGTACCACTCTCCACCATCACCAATTGGGCCAAAGAATTTCGGAAGTGGTTACCTGATATGAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattacacttgcccttgcaatgtaataatacatgcgcttttgttccttgcacagAATGCCCAGCAAATCCATGGTCCTTTTCTTGTAGTTGTTCCATTGTCCACTTTATCAAATTGGGCCAAAGAATTCAGGAAGTGGCTTCCTGATATGAATA
atttgat putative branch site (score: 5)
cgcttttgttcctt putative PPT
aatgtaataatacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagtatctctatttgattacacttgcccttgcaatgtaataatacatgcgcttttgttccttgcacagAATGCCCAGCAAATCCATGGTCCTTTTCTTGTAGTTGTTCCATTGTCCACTTTATCAAATTGGGCCAAAGAATTCAGGAAGTGGCTTCCTGATATGAATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA