Sequence
atgc intronic sequence ATGC exonic sequencegtagttgacaccgttccttttactggtatgtatctatataagaagatagatagatactatgttgatgatgagaatttggattattttctgcagGTTGGTCTTTTGAATGTTGATGGTTACTATAACAATTTGCTTGCTTTCTTTGACACTGGAGTTGAAGAAGGTTTTATTAAACAAGGTGCTTGTAATATCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G26140.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G26140.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 5
gtagttgacaccgttccttttactggtatgtatctatataagaagatagata-gatactatgttgatgatgagaatttggattattttctgcagGTTGGTCTTTTGAATGTTGATGGTTACTATAACAATTTGCTTGCTTTCTTTGACACTGGAGTTGAAGAAGGTTTTATTAAACAAGGTGCTTGTAATATCG
| ||| || ||||||| |||| || || | | ||| | | | || | | || || || | ||||||||||| |||||||||| |||||||||||| ||||||||| || ||||||| ||| ||| |||||||||| ||||| | |||| | ||||| |
----gtaacatagtat-ttttactc---tgta---gtacaaaatctttaatataacaatcaagtgctaactcaaaatt----catactgcacagGTTGGTCTACTGAATGTTGACGGTTACTATAACTGTTTGCTTGCATTATTTGACAATGGTGTTAAAGAAGGTTTCATTAAGCCTTGTGCACGGAATATAG
upper sequence: AT5G26140.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G34510.1 (Glycine max), 3'ss of exon 5
gtagt-tgacaccgttccttttactggtatgtatctatataagaagatagatagatactatgttgatgatgagaatttggattattttctgcagGTTGGTCTTTTGAATGTTGATGGTTACTATAACAATTTGCTTGCTTTCTTTGACACTGGAGTTGAAGAAGGTTTTATTAAACAAGGTGCTTGTAATATCG
||| ||| ||| ||| | | |||| ||| | | | || ||| | ||| | | | || || || ||||||||||| | ||||||||||||||||||||| |||||| || || ||||||| ||| ||||||||||| || ||||| || |||||| | |||||
gtaacctgatgttgttactt--agtagtataaatccttgctatac----------taatataatcatgtgctaactcagaatcatcctccacagGTTGGTCTACTCAATGTTGATGGTTACTATAACTCTTTGCTCGCATTATTTGACAATGGTGTTGAAGAAGGCTTCATTAAGCATGGTGCTCGGAATATAC
upper sequence: AT5G26140.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G05560.1 (Glycine max), 3'ss of exon 5
gtagttgacaccgttccttttactggtatgtatctatataagaagatagata-gatactatgttgatgatgagaatttggattattttctgcagGTTGGTCTTTTGAATGTTGATGGTTACTATAACAATTTGCTTGCTTTCTTTGACACTGGAGTTGAAGAAGGTTTTATTAAACAAGGTGCTTGTAATATCG
| ||| || |||||||| |||| || || | ||| | | | || | | | || || | ||||||||||| |||||||||| |||||||||||| ||||||||| || ||||||| ||| ||| ||||||| || ||||| | |||| | |||| |
----gtaacatagtat-ttttactg---tgta---gtacaaagtctttaatataacaatcaagtgctaactcaatatt----catactgcacagGTTGGTCTACTGAATGTTGACGGTTACTATAACTGTTTGCTTGCATTATTTGACAATGGTGTTAAAGAAGGCTTCATTAAGCCTTGTGCACGGGATATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagaagatagatagatactatgttgatgatgagaatttggattattttctgcagGTTGGTCTTTTGAATGTTGATGGTTACTATAACAATTTGCTTGCTTTCTTTGACACTGGAGTTGAAGAAGGTTTTATTAAACAAGGTGCTTGTAATATCG
tgttgat putative branch site (score: 4)
ttattttct putative PPT
aatttggattatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttgacaccgttccttttactggtatgtatctatataagaagatagatagatactatgttgatgatgagaatttggattattttctgcagGTTGGTCTTTTGAATGTTGATGGTTACTATAACAATTTGCTTGCTTTCTTTGACACTGGAGTTGAAGAAGGTTTTATTAAACAAGGTGCTTGTAATATCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG