Sequence
atgc intronic sequence ATGC exonic sequencegtcgtatataagtcatcagtttctttgatcattctcttagttaacggatatgcaacctatatttcttattgttgttgtgatatatagGAGCTACTATAGATGCACAAACAGCAGATGCACGGTGAAGAAGAGAGTAGAACGTTCATCAGATGATCCATCGATAGTGATCACAACATACGAAGGACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G69310.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G69310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g02060.1 (Oryza sativa), 3'ss of exon 2
------------gtcgtatataagtcatcagtttctttgatcattctcttagttaa--cggatatgcaacctatatttcttattgttgttgtgatatatagGAGCTACTATAGATGCACAAACAGCAGATGCACGGTGAAGAAGAGAGTAGAACGTTCATCAGATGATCCATCGATAGTGATCACAACATACGAAGGACAA
| | | | | | || | |||| |||||| ||||| || ||| | | | | | || | | | | ||||||||||| || ||||| ||||||| ||||||||||||||| | || || || || || || || || || | || ||||| || ||||| || |||
taattagcccccaaactttttttgcaaataaattaatcaatcaatctcttggttaaattaattaattaacatgtgtgtgt-atatataaaaaaaaaaacagGAGCTACTACAGGTGCACGAACAGCAAGTGCACGGTGAAGAAGCGGGTGGAGCGCTCCTCCGACGACCCCTCCGTCGTCATCACCACCTACGAGGGCCAA
upper sequence: AT1G69310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G06870.4 (Glycine max), 3'ss of exon 2
----------gtcgtatataagtcatcagtttctttgatcattctctt-agttaacggatatgcaacctatatttcttattgttgttgtga---tatatagGAGCTACTATAGATGCACAAACAGCAGATGCACGGTGAAGAAGAGAGTAGAACGTTCATCAGATGATCCATCGATAGTGATCACAACATACGAAGGACAA
||| | | || || | | |||| || | || || || | || | | | || || || | | ||||||||||| | ||||||||||||| |||||||||||||||||| || ||||| || || || || ||| |||| ||||| || ||||| ||||| |||
agaacttatgacttcatacatattattcaaa-ctctcaccattaaattgacttcacaacattgataattaattattctgatgcaattatgtctttttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGCTCTTCCGAGGACCCAACGATTGTGATTACTACATATGAAGGGCAA
upper sequence: AT1G69310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G12830.1 (Glycine max), 3'ss of exon 2
-------------gtcgtatataagtcatcagttt--ctttgatcattctcttagttaacggatatgcaacctatatttcttattgttgttgtgatatatagGAGCTACTATAGATGCACAAACAGCAGATGCACGGTGAAGAAGAGAGTAGAACGTTCATCAGATGATCCATCGATAGTGATCACAACATACGAAGGACAA
| ||| | | | | | | || | || | | || | || ||| ||||| || | | | ||||||||||| | ||||||||||||| |||||||||||||||||| || ||||| || || || || ||| | || ||||| || ||||| ||||| |||
tataatgaccacactaatattagaactgttatccaaaccctcaccactaaattgacttcacaacattgcagata-attaattatt-ctgatacattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGGTCTTCCGAGGACCCAACAATTGTGATTACCACATATGAAGGGCAA
upper sequence: AT1G69310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0011g00720.t01 (Vitis vinifera), 3'ss of exon 2
------------gtcgtatataagtc--atcagtttctttgatcattctcttagttaacggatatgcaacctatatttcttattgttgttgtgatatatagGAGCTACTATAGATGCACAAACAGCAGATGCACGGTGAAGAAGAGAGTAGAACGTTCATCAGATGATCCATCGATAGTGATCACAACATACGAAGGACAA
|| | | | || || | || | || || | | | ||| || | ||| || || || | | |||||||| || | ||||||||||||| ||||||||||||||| ||||| ||||| || || || ||||| || || ||||| ||||| ||||| |||
gggatctcttgggttggaaaaaaatcttgttagctagttatatagcagataaattggatttgtattgaaaaaagattaatt-ttattcacacattttgcagGAGCTATTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAAAGAGTTGAACGCTCCTCGGAGGATCCCAGCATCGTAATCACTACATATGAAGGCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcttagttaacggatatgcaacctatatttcttattgttgttgtgatatatagGAGCTACTATAGATGCACAAACAGCAGATGCACGGTGAAGAAGAGAGTAGAACGTTCATCAGATGATCCATCGATAGTGATCACAACATACGAAGGACAA
agttaac putative branch site (score: 3)
tatatttcttattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcgtatataagtcatcagtttctttgatcattctcttagttaacggatatgcaacctatatttcttattgttgttgtgatatatagGAGCTACTATAGATGCACAAACAGCAGATGCACGGTGAAGAAGAGAGTAGAACGTTCATCAGATGATCCATCGATAGTGATCACAACATACGAAGGACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG