Sequence
atgc intronic sequence ATGC exonic sequence...tgatacatttaaaatgtcatgttgatgttctaagtttttcgacagatttgaaaaaattacattagatattttagaaaaattgatgtgttttaataatcagGGATACTGAAGATCATATTGCATGGCTTCTTCAGCACGGGTGGCATGAAAAAGCTTTGGCTGTGGTTGAATCTGGCCAGGGACGGAGTGAACTACTTGAT
Basic information
species | Glycine max |
transcript | GLYMA12G08840.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G08840.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g11880.1 (Oryza sativa), 3'ss of exon 6
-tgatacatttaaaatgtc-atgttgatgttctaagtttttcgacagatttgaaaaaattacat-tagatattttagaaaaattgatgtgt-tttaataatcagGGATACTGAAGATCATATTGCATGGCTTCTTCAGCACGGGTGGCATGAAAAAGCTTTGGCTGTGGTTGAATCTGGCCAGGGACGGAGTGAACTACTTGAT
| | | | | | || || || | || ||| || | ||||| || || | |||||| | | || ||| || ||| || ||| ||||||| |||||| | ||||||||||| || || ||||||||||| || ||||||| |||||| | || || ||||| | || || ||||||
tttgtgtttctgagctttctataaggacatggcaaaattt----catttcagaaaatgttgtatctttatatttctactgatataatatgtgctttcaaattagAGATGCTGAAGACCATATTTCTTGGCTTCTTCAACATGGTTGGCATGAAAAGGCATTGGCTGCAGTTGAAGCAGGACAAGGACGAACCGAGCTTCTTGAT
upper sequence: GLYMA12G08840.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G040247_T01 (Zea mays), 3'ss of exon 6
tgatacatttaaaatgtcatgttgatgttctaagtttttcgacagattt--gaaaaaattacattagatattttagaaaaattgatgtgttttaa------taatcagGGATACTGAAGATCATATTGCATGGCTTCTTCAGCACGGGTGGCATGAAAAAGCTTTGGCTGTGGTTGAATCTGGCCAGGGACGGAGTGAACTACTTGAT
| | | | | | | || ||| ||| | | | |||||| | | || | | ||| || | | | | || || ||| |||||||||||||||| ||||||||||| || || || ||||||||||| ||||||| ||||| | || || ||||| | ||| || ||||||
-------tccattacctttcagtaaaagta-aatcgttttgactgtcctgtggcaaaattttcccaaaaataatcccatgattaatatagtgtgcaccttctgattagAGATGCTGAAGATCATATTGCTTGGCTTCTTCAACATGGTTGCCATGAAAAAGCATTGGCTGCAGTTGAGGCAGGGCAAGGACGCACTGAGCTTCTTGAT
upper sequence: GLYMA12G08840.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0061g00940.t01 (Vitis vinifera), 3'ss of exon 6
tgatacatttaaaatgtcatgttgatgttctaagtttttcgacagatttgaaaaa-attacattagatattttagaaaaattgatgtgttttaataatc-agGGATACTGAAGATCATATTGCATGGCTTCTTCAGCACGGGTGGCATGAAAAAGCTTTGGCTGTGGTTGAATCTGGCCAGGGACGGAGTGAACTACTTGAT
| | ||| || | | | | ||| | | || | | | | ||| | | | ||| | | || || || ||| |||||| | | |||||| ||||||||||||| | ||||| ||||| || |||||||||||||||||||| || | |||||| | || || || ||||||||||| ||||||
taaggtgttttc--tgccgttatattcttcaatactattttaaaaaatagaatatcacaaaatttgtttgatttgagaagcaaatgcgttttatgattttagGGATGCTGAAGATCATATCTCTTGGCTCCTTCAACATGGGTGGCATGAAAAAGCTTTAGCAGCAGTTGAAGCAGGGCAAGGGCGGAGTGAACTCCTTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgaaaaaattacattagatattttagaaaaattgatgtgttttaataatcagGGATACTGAAGATCATATTGCATGGCTTCTTCAGCACGGGTGGCATGAAAAAGCTTTGGCTGTGGTTGAATCTGGCCAGGGACGGAGTGAACTACTTGAT
ttttaat putative branch site (score: 3)
attagatattttagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgatacatttaaaatgtcatgttgatgttctaagtttttcgacagatttgaaaaaattacattagatattttagaaaaattgatgtgttttaataatcagGGATACTGAAGATCATATTGCATGGCTTCTTCAGCACGGGTGGCATGAAAAAGCTTTGGCTGTGGTTGAATCTGGCCAGGGACGGAGTGAACTACTTGAT
- - - - - - - - - - gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtg