Sequence
atgc intronic sequence ATGC exonic sequence...attagaaggctaactgtttcagttatcagatcaccttcatttgcatgcaatccatgcatgttttacatttttccctgttttggcttattgttatatttagGCCCTCTTTCGAAAAATTGCTGCTGCATTACCTGGAATGGAAACACTATCCTCCACAAAACAAGAAGATATGGTTGACGTGAACCTAAGATCTTCTGGTG
Basic information
species | Glycine max |
transcript | GLYMA01G41090.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G41090.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0012g00790.t01 (Vitis vinifera), 3'ss of exon 2
--------attagaaggctaactgtttcagttatcagatcaccttcatttgcatgcaatccatgcatgttttacatttttccctgttttggcttattgttat-atttagGCCCTCTTTCGAAAAATTGCTGCTGCATTACCTGGAATGGAAACACTATCCTCCACAAAACAAGAAGATATGGTTGACGTGAACCTAAGATCTTCTGGTG---
|| | | | || | | || | ||| | | || || || | | | ||| || || | || | || |||| || |||| |||||||| ||| ||||| |||||||||||||| || || | || |||||||| |||||||| |||||||||| ||| | |
gtaatctctttccccagacatcctttagattaattcttggatgctcactaggttgtaac---tgtcttgatcatggaattctttggttaaatgaacctttttcatacagGCACTGTTTCAGAAAATTGCAGCT---TTACCAGGAATGGAAACACTTTCTTCAGCCAAGCAAGAAGACATGGTTGATGTGAACCTAAAGTCTCCCAGCCTCA
upper sequence: GLYMA01G41090.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S39_147V6.2 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------------------------------------------------attagaaggctaact---gtttcagttatcagatcaccttcatttgcatgcaat------ccatgcatgttttacatttttccctgttttggcttatt-------gttatatttagGCCCTCTTTCGAAAAATTGCTGCTGCATTACCTGGAATGGAAACACTATCCTCCACAAAACAAGAAGATATGGTTGACGTGAACCTAAGATCTTCTGGTG----
||| || | |||| | | || | ||| |||| || | | | || | | |||| || ||| | | || |||| || |||||||||||||||||||| || ||||||||||| || | || || || || || || | ||||| || || || | | || | | |
gtaaatctctttccggcttgaactgtgtatttgtacagattttatattccgaggaggtaatttacaatttttgagtagatggaattgtgcatctgatgcaagtttaactcgctagcttgtctttctttgggcataaaaatgagctaggtctgctcagtgtaattccaccaggcatctcattttggaacatcacatgcagGCACTGTTTCGAAAAATTGCTGCTGCGTTGCCTGGAATGGAGACTATGTCTTCT-CACAA--GGATGACCTTGTTGATGTTAATCTTAAACCTAC-GTTAAATA
upper sequence: GLYMA01G41090.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S456_9V6.1 (Physcomitrella patens), 3'ss of exon 6
--attagaaggctaactgtttcagttatcagatcaccttcatttgcatgcaatccatgcatgttttac-atttttccctgttt-tggcttattgttatatttagGCCCTCTTTCGAAAAATTGCTGCTGCATTACCTGGAATGGAAACACTATCCTCCACAAAACAAGAAGATATGGTTGACGTGAACCTAAGATCTTCTGGTG---
|| | ||| || ||| || | | | ||||| || | | | || || || | | | | || | | | |||| || ||||||||||||||||| ||||||||||| ||||| | | || || || || || ||| | ||||| || || || | | |
gcatacgttttgatacttattaggttttcgtagcgc--tcatt-atatatagctt-taaaagtgcaaccataccatacagctcatataatactatatcgtgcagGCACTGTTTCGAAAAATTGCTGCAGCATTACCTGGTATGGAGGCTTTGTCATCT-CACAA--GGATGATCTTGTTGATGTCAATCTCAAGCCAACAACAAACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcaatccatgcatgttttacatttttccctgttttggcttattgttatatttagGCCCTCTTTCGAAAAATTGCTGCTGCATTACCTGGAATGGAAACACTATCCTCCACAAAACAAGAAGATATGGTTGACGTGAACCTAAGATCTTCTGGTG
ttattgttatattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attagaaggctaactgtttcagttatcagatcaccttcatttgcatgcaatccatgcatgttttacatttttccctgttttggcttattgttatatttagGCCCTCTTTCGAAAAATTGCTGCTGCATTACCTGGAATGGAAACACTATCCTCCACAAAACAAGAAGATATGGTTGACGTGAACCTAAGATCTTCTGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - gctaact
- - - - - - - - - - - - - - - -caccttc
- - - - - - - - - - - - - - - - - - - - - gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - -ccatgca