Sequence
atgc intronic sequence ATGC exonic sequencegttcgtacattcatttcattagtcctctgtttaagatacaaaaatattgagtctaaatgtctaactaatattatttttggggtgatttttttcagACGGAGGTTATGTGTTTGGGAAAACTAAAGCATCCGAATCTGGTGAAGCTGATCGGATATTGCTGCGAGGAAGCACATAGACTTCTTGTTTATGAGTTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G35580.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G35580.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G17050.1 (Glycine max), 3'ss of exon 1
gttcgtacat-tcatttcattagtcctctgtttaagatacaaaa-atattgagt--ctaaatgtctaactaatattatttttggggtgattttttt-cagACGGAGGTTATGTGTTTGGGAAAACTAAAGCATCCGAATCTGGTGAAGCTGATCGGATATTGCTGCGAGGAAGCACATAGACTTCTTGTTTATGAGTTCA
|| | | | | |||| || | | | | || | | ||||| | || | | | || | || ||| ||||| || ||| ||| | |||| |||||| |||||| |||||||||||||||| ||||||||||| || |||| ||| || ||||| || |||||||
tttattgcttatgattttgttgattagttatgaagaatccttttcgcaatgagtgcttttgagttgagttctgaccatcccttttgttttttgacgacagACTGAAGTTGTGTTTCTGGGTCAACTAAGGCATCCACATCTGGTGAAGCTGATTGGATATTGCTGTGAAGAAGAACACAGGCTTCTGGTATATGAGTATT
upper sequence: AT5G35580.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G05660.1 (Glycine max), 3'ss of exon 1
-gttcgtacat-tcatttcattagtcctctgtttaagatacaaaaatattgagtctaaatgtctaactaatattatttttggggtgattttttt-----cagACGGAGGTTATGTGTTTGGGAAAACTAAAGCATCCGAATCTGGTGAAGCTGATCGGATATTGCTGCGAGGAAGCACATAGACTTCTTGTTTATGAGTTCA
|| | | | | |||| || | | | || | || | || ||| || | | | | || | ||||||| ||||| || ||| ||| | |||| |||||| |||||| |||| ||||||||||| ||||||||||| || |||| ||| || ||||| || |||||||
atttattgcttatgattttcttgattaattat--gaggaataatcctttttgcaataagtgcttctgagttctgaccttcccttttgtttttttgacgacagACTGAAGTTGTGTTTCTGGGTCAACTAAGGCATCCACATCTCGTGAAGCTGATTGGATATTGCTGTGAAGAAGAACACAGGCTTCTGGTATATGAGTATT
upper sequence: AT5G35580.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S207_2V6.1 (Physcomitrella patens), 3'ss of exon 2
-----gttcgtacattcatttcattagtcctctgtttaagatacaaaaatattgagtctaaatgtctaactaatattatttttggggtgattttttt-cagACGGAGGTTATGTGTTTGGGAAAACTAAAGCATCCGAATCTGGTGAAGCTGATCGGATATTGCTGCGAGGAAGCACATAGACTTCTTGTTTATGAGTTCA
| ||| || | | || || || | | | || ||| ||| | | || | || || | | ||| | || |||| | | | || | || | ||||||||||| |||||||| || |||||||||| |||||| | || | || || ||||| || ||||
aagtagaaggtagggaatctttaaatatttcctactttagtgattcagctctt-agttcaaacagaccggcacttacatagacgtcgttatcgtaatgcagGCTGAAGTTAATTTTCTTGGTCAGCTTCACCATCCGAATCTCGTGAAGCTCATTGGATATTGCTCCGAGGATGATCAACGCCTGCTGGTTTACGAATTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaatattgagtctaaatgtctaactaatattatttttggggtgatttttttcagACGGAGGTTATGTGTTTGGGAAAACTAAAGCATCCGAATCTGGTGAAGCTGATCGGATATTGCTGCGAGGAAGCACATAGACTTCTTGTTTATGAGTTCA
aactaat putative branch site (score: 2)
tttttttc putative PPT
tctaaatgtctaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgtacattcatttcattagtcctctgtttaagatacaaaaatattgagtctaaatgtctaactaatattatttttggggtgatttttttcagACGGAGGTTATGTGTTTGGGAAAACTAAAGCATCCGAATCTGGTGAAGCTGATCGGATATTGCTGCGAGGAAGCACATAGACTTCTTGTTTATGAGTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC