Sequence
atgc intronic sequence ATGC exonic sequence...tgataatgtgactgttagaccaagaataggtttaaggttaaagattttgtatttttattttttagaaatttctaaccagccttctccttcaccttcacagGTGGCAGAGTGGGGAATGATGAGTATGTGTGATGCTGAAAGAAGACTTCTGGCTAATGCATTGCTTGATATCTCAAATGAATGGTTTATCCTCTTATCGG
Basic information
species | Glycine max |
transcript | GLYMA08G21100.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G21100.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G21310.1 (Arabidopsis thaliana), 3'ss of exon 3
tgataatgtgactgttagaccaagaataggtttaaggttaaagattttgtatttttattttttagaaatttctaaccagccttctccttcaccttcacagGTGGCAGAGTGGGGAATGATGAGTATGTGTGATGCTGAAAGAAGACTTCTGGCTAATGCATTGCTTGATATCTCAAATGAATGGTTTATCCTCTTATCGG
| |||| | | | | |||| ||| | |||| | || |||| | | | || || | | || | || | || |||||| |||||||||||||||||||||||| || ||| ||||||| || ||||| |||||||| || ||||||||| | | |||| |
-----gtacttttgttgatcaatgta-----ttaatgttgc--ttcttgtgtcttgatttggtttatctcacttcggagtttctttatttg--tgtgtagCATGTAGCTTGGGGAGAGATGAGTATGTGTGATGCTGAAAGGAGGCTTTTGGCTAACGCGTTGCTCGATATCTCTAACGAATGGTTTGTTTTACTATCTG
upper sequence: GLYMA08G21100.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G51770.2 (Arabidopsis thaliana), 3'ss of exon 1
tgataatgtgactgttagaccaagaataggtttaaggttaaagattttgtatttttattttttagaaatttctaaccagccttctccttcaccttcacagGTGGCAGAGTGGGGAATGATGAGTATGTGTGATGCTGAAAGAAGACTTCTGGCTAATGCATTGCTTGATATCTCAAATGAATGGTTTATCCTCTTATCGG
|| || || | ||| || | || | | ||| ||| || | | || | | | || | || | ||| | | |||||| |||||||||| |||| || || || || ||| |||||||||| |||||||||||||| ||||||||
-------------gtactgtcattgatgtttcagaggaaaatcttgttttgtgtttgtttctt-gtgttctcacagtattagtttcttctgtgtt-atagGCTGTGGCATGGGGAGAGATGAGTATGGGTGAAGCAGAGAGGAGGCTTTTGGCTAATGCGTTGCTTGATATCTCTAATGAATG-----------------
upper sequence: GLYMA08G21100.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G51770.1 (Arabidopsis thaliana), 3'ss of exon 1
tgataatgtgactgttagaccaagaataggtttaaggttaaagattttgtatttttattttttagaaatttctaaccagccttctccttcaccttcacagGTGGCAGAGTGGGGAATGATGAGTATGTGTGATGCTGAAAGAAGACTTCTGGCTAATGCATTGCTTGATATCTCAAATGAATGGTTTATCCTCTTATCGG
|| || || | ||| || | || | | ||| ||| || | | || | | | || | || | ||| | | |||||| |||||||||| |||| || || || || ||| |||||||||| |||||||||||||| |||||||||||| | || | || |
-------------gtactgtcattgatgtttcagaggaaaatcttgttttgtgtttgtttctt-gtgttctcacagtattagtttcttctgtgtt-atagGCTGTGGCATGGGGAGAGATGAGTATGGGTGAAGCAGAGAGGAGGCTTTTGGCTAATGCGTTGCTTGATATCTCTAATGAATGGTTTGTTCTGCTGTCTG
upper sequence: GLYMA08G21100.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0002g02660.t01 (Vitis vinifera), 3'ss of exon 1
tgataatgtgactgttagaccaagaataggtttaaggttaa-agattttgtat-ttttattttttagaaatttctaaccagccttctccttcaccttcacagGTGGCAGAGTGGGGAATGATGAGTATGTGTGATGCTGAAAGAAGACTTCTGGCTAATGCATTGCTTGATATCTCAAATGAATGGTTTATCCTCTTATCGG
| ||| | || | || || | | || | || | ||| | | | |||| || | || | | || ||||||| ||||||||||||||||| |||||||||||||| || ||||| || |||||||||||||||||||| ||||||||||| |||||||| || |
-tccagtgtctcaacacccccttaagcgtattctcatttgacatgttctctagactctatggctggaacagttcttactcttgtgcttgtct-catttgcagGTGGTGGAGTGGGGAATGATGAGCATGTGTGATGCTGAGAGGAGACTACTAGCTAATGCATTGCTTGATATTGACAATGAATGGTTCATCCTCTTGTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtatttttattttttagaaatttctaaccagccttctccttcaccttcacagGTGGCAGAGTGGGGAATGATGAGTATGTGTGATGCTGAAAGAAGACTTCTGGCTAATGCATTGCTTGATATCTCAAATGAATGGTTTATCCTCTTATCGG
ttctaac putative branch site (score: 1)
ccagccttctccttca CT-rich tract
atttttattttttaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgataatgtgactgttagaccaagaataggtttaaggttaaagattttgtatttttattttttagaaatttctaaccagccttctccttcaccttcacagGTGGCAGAGTGGGGAATGATGAGTATGTGTGATGCTGAAAGAAGACTTCTGGCTAATGCATTGCTTGATATCTCAAATGAATGGTTTATCCTCTTATCGG
- - - -gtgactg
- - - - - - - - - -ccaagaa