Sequence
atgc intronic sequence ATGC exonic sequence...aattgagtaaaatagatgtattttatctttatttatgaacgccgtacaattgaaattaataatattgatgccaaaaagaaatgaatgaaaatgtggacagGAGCAACAGGGAAGACGGTGGCAATAATAGTAGGAGGAGCAGCTGGTGTTGGCTTTCTTGTCATTTGCTTGCTTTTTGCCAAAAACTTGATGAGGAAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04520.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G34230.1 (Glycine max), 3'ss of exon 1
-aattgagtaaaatagatgt--attttatctttatttatgaacgccgtacaattgaaattaataatattgatgccaaaaaga-aatgaatgaaaatgtggacagGAGCAACAGGGAAGACGGTGGCAATAATAGTAGGAGGAGCAGCTGGTGTTGGCTTTCTTGTCATTTGCTTGCTTTTTGCCAAAAACTTGATGAGGAAGAA
| | | |||| | || | | || | ||| ||| || || || || | ||| ||| || | | | | |||||||||| ||||| |||||||||||||| |||||||| || | ||| | ||||| |||||| | ||||| | | |||| || |||
ttgtctatttgtgccaatgttaaaaaaatgtgcgactttgctcaatgtagaatatggtttgattatgagtgtgatgtgtggctaattgatgcaatggcagGGCAAAATA-CAGGGAAGACAGTGGCTATAATAGTAGGAGGGGCAGCTGGAGTGGCGTTTTTGGTCATATGCTTGATGTTTGCTAGGAGTTTGAAGAAGAA---
upper sequence: AT1G04520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G33410.1 (Glycine max), 3'ss of exon 1
---aattgagt-aaaatagatgtattttatctttatttatgaacgccg--tacaattgaaattaataatattgatgccaaaaagaaatgaatgaaaatgtggacagGAGCAACAGGGAAGACGGTGGCAATAATAGTAGGAGGAGCAGCTGGTGTTGGCTTTCTTGTCATTTGCTTGCTTTTTGCCAAAAACTTGATGAGGAAGAA
| ||| | || | | | | | | | || | || | | || || | ||| || ||||| ||| ||| || | | | |||||||||| ||||| |||||| ||||||| |||||||| || | ||| | || || |||||| | ||||| | | |||| || |||
tctatttgtgccaatgttcaaaaaatgtgccact-ttgctcaatgtggattatggtttga-ttatgaagtgtgatgtgtgtggttaattgatgcaatgacagGGCAAAATA-CAGGGAAGACAGTGGCTATAATATTAGGAGGGGCAGCTGGGGTGGCGTTTTTGGTTATATGCTTGATGTTTGCTAGGAGTTTGAAGAAGAA--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaattgaaattaataatattgatgccaaaaagaaatgaatgaaaatgtggacagGAGCAACAGGGAAGACGGTGGCAATAATAGTAGGAGGAGCAGCTGGTGTTGGCTTTCTTGTCATTTGCTTGCTTTTTGCCAAAAACTTGATGAGGAAGAA
tattgat putative branch site (score: 3)
tgaaattaataatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattgagtaaaatagatgtattttatctttatttatgaacgccgtacaattgaaattaataatattgatgccaaaaagaaatgaatgaaaatgtggacagGAGCAACAGGGAAGACGGTGGCAATAATAGTAGGAGGAGCAGCTGGTGTTGGCTTTCTTGTCATTTGCTTGCTTTTTGCCAAAAACTTGATGAGGAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - -aaataga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgaaa