Sequence
atgc intronic sequence ATGC exonic sequencegtatgtacatctctctattaggtgttttgtgttaaaagtttcacctcattgtcttggaaggcatataatctttctcatattaaggcttggttgtgttctcttgcagttaaaagacttttggtagctgtgattttttgctttcctctaaagattctgagaaactcttttatctcaaatgttgtagATATTTGGTGGTGTTGGTATTGCTTGCCTACCCTTGGGCCTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G01460.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
gtatgtacatctctctattaggtgttttgtgttaaaagtttcacctcattgtcttggaaggcatataatctttctcatattaaggcttggttgtgttctcttgcagttaaaagacttttggtagctgtgatttt-ttgctttcct-ctaaagattctgagaaactcttttatctcaaatgttgtagATATTTGGTGGTGTTGGTATTGCTTGCCTACCCTTGGGCCTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG
|| | | || | || | ||| | | ||| | ||| || | || | | |||| | ||| | | | ||||||||||||||||||||| ||||||||||| || ||||| ||||| |||| || |||| ||||| ||||| || || || ||||| |||||||||
-------------------------------------------------------------------------------------ctgtactagaaacaatttgaaatatggatcctttccaacatccaattctgctgcaatcatgctggtttctttttacaactttcctattcctgtt-tggtagATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG
upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G30400.1 (Glycine max), 3'ss of exon 4
gtatgtacatctctctattaggtgttttgtgttaaaagtttcacctcattgtcttggaaggcatataatctttctcatattaaggcttggttgtgttctcttgcagttaaaagactttt-ggtagctgtgattttttgctttcct-ctaaagattctgagaaactcttttatctcaaatgttgtagATATTTGGTGGTGTTGGTATTGCTTGCCTACCCTTGGGCCTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG
| ||| | | || | ||| | | |||| |||| | || ||| | | || ||| | || | |||||||||||||||||||||||||||| || || ||||| ||||| | ||||||| |||| |||||||||||||||||||| ||||||||||| |||
--------------------------------------------------------------------------------------taaactgtacaaaagaagaatcaattacttcccaggtcatatttacttttatttttcatattagtgatattaacaattgttttctttccattcaatccagATATTTGGTGGTGTTGGTATTGCTTGTCTTCCATTGGGACTTATATTTTCATTCATTCGGCGTCCAAAGGCTGTTATCACTCGTTCACAGTATATCAAG
upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 4
gtatgtacatctctctattaggtgttttgtgttaaaagtttcacctcattgtcttggaaggcatataatctttctcatattaaggcttggttgtgttctcttgcagttaaaagacttttggtagctgtgattttttgctttcctctaaagattctgagaaactcttttatctcaaatgttgtagATATTTGGTGGTGTTGGTATTGCTTGCCTACCCTTGGGCCTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG
|||| | | | | ||| | | | | | | |||| | || || ||| | | ||| | || | |||||||||||||||||||||||||||| || || ||||| ||||| | ||||||| | || |||||||||||||||||||| ||||||||||| |||
-----------------------------------------------------------------------------------tacttg-taataactttctaaagtcttcaatcccaggtcacatttacttttatttttcatattagtgatatcaactattgttttctttccattcaatccagATATTTGGTGGTGTTGGTATTGCTTGTCTTCCATTGGGACTTATATTTTCATTCATTCGACGTCCAAAGGCTGTTATCACTCGTTCACAGTATATCAAG
upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 4
gtatgtacatctctctattaggtgttttgtgttaaaagtttcacctcattgtcttggaaggcatataatctttctcatattaaggcttggttgtgttctcttgcagttaaaagacttttggtagctgtgattttttgctttcctctaaagattctgagaaactcttttatctcaaat-gttgtagATATTTGGTGGTGTTGGTATTGCTTGCCTACCCTTGGGCCTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG
| || || | | || | | |||| || || ||| | |||| | ||| | ||| | | | | |||| || | | | ||||||||||||||||||||||||| || || || || || ||||| | |||| || |||| |||||||||||||||||||| ||||||||||| |||
--------------------------------------------------------------------------taatggatttatttaaataagc-ctttcata-ctaaatcacattaagtactt----cttttcccattctt-----gatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCACAGTATATCAAG
upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtacatctctctattaggtgttttgtgttaaaagtttcacctcattgtcttggaaggcatataatctttctcatattaaggcttggttgtgttctcttgcagttaaaagact---tttggtagctgtgattttttgctttcctctaaag-attctgagaaactcttttatctcaaatgttgta----gATATTTGGTGGTGTTGGTATTGCTTGCCTACCCTTGGGCCTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG
| | | | | || || | ||| | ||| |||||| |||| |||| ||| | | |||||| | ||||| || ||||||||| || |||||||||||||| | || ||||| ||||| | ||||||| |||| || |||||||||||||| || ||||||||||| |||
--------------------------------------------------------------------------------------------gagataggataaaattggaaagttatgttttagatctggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttttgctttcctctaaagattctgagaaactcttttatctcaaatgttgtagATATTTGGTGGTGTTGGTATTGCTTGCCTACCCTTGGGCCTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG
ctctaaa putative branch site (score: 3)
taaagatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtacatctctctattaggtgttttgtgttaaaagtttcacctcattgtcttggaaggcatataatctttctcatattaaggcttggttgtgttctcttgcagttaaaagacttttggtagctgtgattttttgctttcctctaaagattctgagaaactcttttatctcaaatgttgtagATATTTGGTGGTGTTGGTATTGCTTGCCTACCCTTGGGCCTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT