Sequence
atgc intronic sequence ATGC exonic sequence...aatgatgttcatcgcctgattaggaaaccattttatgggtttaatctttgagatattgttgtgggaatcattaaccaagcatacggaggcattattacagGTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53620.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G35710.1 (Glycine max), 3'ss of exon 5
aatgatgtt-catcgcctgattaggaaaccattttatgggtttaatctttgagatattgttgtgggaatcattaaccaa-gcatacggaggcattattacagGTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAG
|| |||| || || | | ||| | | ||| | ||| | | ||| | || ||| || | | || | |||| |||||| ||||||| || |||||||||||||||||||||||||| ||||||| |||| || || |||
-ttgttgttatatttccaaaggacaaaaaaaaagatttttttttctttttcaaagattac-atttgagcaatttgttaatgtaagttgactgaatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAGTCGGGGCTTATCAAG
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G33000.6 (Glycine max), 3'ss of exon 5
-aatgatgttcatcgcctgattaggaaaccattttatgggtttaatctttgagatattgttgtgggaatcattaaccaagcatacggaggcattattacagGTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAG
| | || || | | | || | | | ||| | ||| | |||| | | || | | | || | |||| |||||| ||||||| || |||||||||||||||||||||||||| ||||||| ||||||| || |||
tactaatatt-gttatatttccaaaggacaaaaaaaagatttttttttttcaaatatcacctttgagcaatttgttaatgtaacttgattaaatatttcagGTGATTGAGATTGGGAAAGGGAGCAAGGTGAAATATGAACTGGACAAAAAATCGGGTCTTATCAAG
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 3
--aatgatgttcatcgcctga--ttaggaaaccattttatgggtttaatct-ttgagatattgttgtgggaatcattaaccaagcatacggaggcattattacagGTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAG
|| ||||| || ||| ||| || | | || ||| |||||| ||| | | | | | || ||| | | || || |||||||| || ||||| ||||| |||||||||||||||||||| ||||||| || || || |||| |
catatcatgttgttcctgtgaccttaaattgttatgatttttattgcctctattgagaaattagacttgaa--tacttgtgaa--atattgctgaatc-ttgcagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 3
--aatgatgttcatcgcctgattaggaaaccattttatgggtttaatctttgagatattgttgtgggaatcattaaccaa--gcatacggaggcattattacagGTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAG
|| ||||| || ||| || | ||||| ||| || | || | | ||| | || | ||| || | || || ||||||||||| || || ||||| || ||||||||||||||||| ||||||| || ||||| |||| |
catatcatgttgttcttgtgaccttaaat---tgttatgaattttattgtctctattgagaaattggatttgaatacttatgaaatattgatgaatc-ttgcagGTGGTTGAAATTGGGAAAGGAAGTAAGGTGAAATATGAACTTGACAAAAGAACTGGTCTTATTATG
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 3
---aatgatgttcatcgcctgattaggaaaccattttatgggtttaatctttgagatattgtt--gtgggaatcattaaccaagcatacggaggcattattacagGTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAG
| ||| || | || ||| | || | | || | ||| | || | | ||| | |||| | ||| || ||||||||||| ||||| |||||||||||||||||||||||||| ||||| | || || || || |||
actagtgaaatttgacaaaattttcataaataaattgttag----aaaccttgccttcttaatcaaccaaggttcttatttgaacatatgtcta-atttttgcagGTGGTTGAAATAGGGAAAGGGAGCAAGGTGAAATATGAACTTGACAAGAAAACTGGACTGATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgagatattgttgtgggaatcattaaccaagcatacggaggcattattacagGTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAG
cattaac putative branch site (score: 2)
aatcattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgatgttcatcgcctgattaggaaaccattttatgggtttaatctttgagatattgttgtgggaatcattaaccaagcatacggaggcattattacagGTGGTTGAGATAGGAAAAGGGAGCAAGGTGAAATATGAACTCGACAAAACTACGGGTCTCATTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - aaaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccaag