Sequence
atgc intronic sequence ATGC exonic sequence...gaaggtcctttggatatagaaacacaataaaaaaattgtgaaatccggttttggtgtttggactcaaataatatttgggtatggtttggtatggtgacagGTATAGGCATCTGGGACAATTTGCACCACTGGGAGGGGAGCAAACGGCAGCACAACTTCCAGGAGATTGGGTTTCTATTGGACACAGCAGCCAGTGGCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G05020.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G05020.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G145972_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------------gaaggtcctttgg-atatagaaacacaataaaaaaattgtgaaatccggttttggtgtttggactcaaataatatttgggtatggtttggtatggtgacagGTATAGGCATCTGGGACAATTTGCACCACTGGGAGGGGAGCAAACGGCAGCACAACTTCCAGGAGATTGGGTTTCTATTGGACACAGCAGCCAGTGGCTC
|| | || | || | | |||| | || | |||| ||| | || |||| | || ||| | |||||| |||||||||| ||||| || ||||| |||||||||||||| || ||||| ||||| || || ||| | || ||||| |||||| ||||||||||
gtttcctattccaccactcatttgctcaatgtttccatagttggctcttcactctgatccaaatgctgttcgccatgcctttgccctcctccaaaagcatcaacttt--tttttctgtacagcagcatctaatgctat----tgcttttctgaccctccagGTACCGGCATCTGGGCCAATTCGCCCCACTAGGAGGGGAGCAAACTGCTGCACAGCTTCCCGGGGACTGGATCTCCATTGGCCACAGCTCCCAGTGGCTC
upper sequence: AT4G05020.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G30920.2 (Glycine max), 3'ss of exon 8
-----------------------------------gaaggtcctttggatatagaaacacaataaaaaaattgtgaaatccg---gttttggtgtttggac-----tcaaataatatttgggtatggtttggt--atggtgac---agGTATAGGCATCTGGGACAATTTGCACCACTGGGAGGGGAGCAAACGGCAGCACAACTTCCAGGAGATTGGGTTTCTATTGGACACAGCAGCCAGTGGCTC
| | | || | | | | || ||| || || ||| || |||| | | |||| | | || |||| || || | ||||| | |||| | || |||||||| || || ||||| |||||||| || ||||| ||||| || ||||||||||| |||||||||||| || |||||
gtaacatgatcatattaatttactagctttgcttttatgtgctctttactttcacatgatgatgaaatgatcaatggttctatgtttttcattggttggtcaatgtttttctaatttctcattactacatggttgattgttcctcaagGTACAAGCATTTAGGTCAATTTGCTCCTCTAGGAGGAGAGCAAACAGCTGCACAGCTTCCTGGGGATTGGGTTTCAATTGGACACAGCTCTCAATGGCTG
upper sequence: AT4G05020.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G06380.1 (Glycine max), 3'ss of exon 8
-----------------------------------gaaggtcctttggatatagaaacacaataaaaaaattgtgaaatccgg---ttttggtgtttggac----tcaaataatatttgg-----gtatggtttggtatggtgacagGTATAGGCATCTGGGACAATTTGCACCACTGGGAGGGGAGCAAACGGCAGCACAACTTCCAGGAGATTGGGTTTCTATTGGACACAGCAGCCAGTGGCTC
| | | || | | | | || ||| || | || ||| || |||| | | |||| | | |||||| | | ||||| | |||| | || ||||| || || || ||||| |||||||| || ||||| ||||| || ||||||||||| |||||||||||| || ||| |
gtagcatgatcatattagtttactagctttgcttttatgtgctctttactttcacatgatgatgaaatgatcaatgattcaatgtttttcattggttggtcaatgttttctaatttctcataactacatggttgattgttcctcaagGTACAAGCATTTAGGTCAATTCGCTCCTCTAGGAGGAGAGCAAACAGCTGCACAGCTTCCTGGGGATTGGGTTTCAATTGGACACAGCTCTCAATGGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggttttggtgtttggactcaaataatatttgggtatggtttggtatggtgacagGTATAGGCATCTGGGACAATTTGCACCACTGGGAGGGGAGCAAACGGCAGCACAACTTCCAGGAGATTGGGTTTCTATTGGACACAGCAGCCAGTGGCTC
actcaaataatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaggtcctttggatatagaaacacaataaaaaaattgtgaaatccggttttggtgtttggactcaaataatatttgggtatggtttggtatggtgacagGTATAGGCATCTGGGACAATTTGCACCACTGGGAGGGGAGCAAACGGCAGCACAACTTCCAGGAGATTGGGTTTCTATTGGACACAGCAGCCAGTGGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT