Sequence
atgc intronic sequence ATGC exonic sequencegttatacgcatctcgtatcattacttaagtgttattttatctgttgatatctatggcaatatgtgaaatattgaaatgttgtgtgttgtagCCTGGTCCGGATTCGGTTGGCATCTTTGCCATTTCGCAAAGATGCAATGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGCTTAGAACCTATGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G60690.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G042250_T03 (Zea mays), 3'ss of exon 5
gttatacgcatctcgtatcattacttaagtgttattttatctgttgatatctatggcaatatgtgaaatattg---aaatgttgtgtgttg--tagCCTGGTCCGGATTCGGTTGGCATCTTTGCCATTTCGCAAAGATGCAATGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGCTTAGAACCTATGAAG
|||||| | || | ||| | ||| || ||| | | | || | | || | | | | || |||| | || ||||||||||||||||||||||| || | ||||||||||| | ||| ||| || || || || ||||||||| | || | ||||||| | ||
gttataag--tcaactctcaattcttgttctttcccttaagttacattttttacagataagtgctacttgctaactacattttgttttctgattagCCTGGTCCGGATTCGGTTGGTATTGTGGCCATTTCGCATGGTTGCCGTGGCGTTGCTGCCCGCGCCTGTGGTTTGGTGAATCTAGAACCAACAAAA
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------gttat-acgcatctcgtatcattacttaagtgttatttt--atctgttgatatctatggcaatatgtgaaa-tattgaaatgttgtgtgttgt-agCCTGGTCCGGATTCGGTTGGCATCTTTGCCATTTCGCAAAGATGCAATGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGCTTAGAACCTATGAAG
||||| | || || | ||| ||| | ||| || | ||| | |||| | | || ||| ||| | | ||| |||||||||||||||||||||| |||||||||||||| ||||| |||| ||||||||||||||||||||||||||||||||| |||||||||| ||||
gtttcttttttctgttccttgcaatgaatttgttaagaaattggtggcctttggcatctagaggatagttattgtgaatttcattgtgatac---ggtgctgatttgaatttactgaatttgccaattatatcttcatctaaaaaaaagttctattttgccagCCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACAAAGTTGCAGTGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGTTTAGAACCTACGAAG
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------------gttatacgcatctcgtatcattacttaagtgttattttatctgttgatatctatggcaatatgtgaaatattgaaatgttgtgtgttgtagCCTGGTCCGGATTCGGTTGGCATCTTTGCCATTTCGCAAAGATGCAATGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGCTTAGAACCTATGAAG
|| | | || |||| ||| | | | ||| ||| | || || | | | || ||| ||| | | | |||||||||||||||||||||| |||||||||||||| ||||| |||| ||||||||||||||||||||||||||||||||| |||||||||| |||
gttttttttttcttttctgttccttgcaatgaatttgttaagaaattggtgacctttggcatctagaggacagcttttgtgaatttcgttgtgataccccgttttgaattt-tctaaatttgtcaat--tatctcttcatctaagaaaaagttctttttgccagCCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACAAAGTTGCAGTGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGTTTAGAACCTACAAAG
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------gttatacgcatctcgtatcattacttaagtgttattttatc-tgttga----tatctatggcaatatgtgaaatattgaaatgttgtgtgttgt-agCCTGGTCCGGATTCGGTTGGCATCTTTGCCATTTCGCAAAGATGCAATGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGCTTAGAACCTATGAAG
|||| || | | | || | | | | ||| || ||| | ||| | || ||| ||| ||| ||||| || ||| |||||||||||||||||||||| |||||||||||||| || || |||| |||||||||||||||||| || |||||||| || |||||||| |||
gttttgcattttcttctataaagaattgttttcttcttcattctatatgcttttattgatatagtgtgtttctcacaatataatgctgaagcgtttctgagttgat-tgtttaattttg--ttgttg-atgctgtcagCCTGGTCCGGATTCGGTTGGGATCTTTGCCATTTCACATAGTTGCAGTGGAGTGGCAGCTCGAGCATGCGGTCTTGTAAGTTTAGAACCCTCAAAG
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0019g04320.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------------------------------------gttatacgcatctcgtatcattacttaagtgttattttatctgttgatatctatggcaat-atgtgaaatattgaaatgttgtgtgt-tgtagCCTGGTCCGGATTCGGTTGGCATCTTTGCCATTTCGCAAAGATGCAATGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGCTTAGAACCTATGAAG
| || | | | ||||| | || || || ||||| | | | || || | | | | | | | | || | ||||||||||||||||||| || | |||||||||| || || ||||||||||||||||| |||||||| ||||||| |||||||||| ||
gtatttttttatattatcttcatatatttatatctatacatgtgtggtgtgcaagtgtgttgcattacattgattcaaactttaggttttacttatcaa-atgtatgtttttcattatccttgtagagctgactcatttacatcttgtgcttgtttctcttttgagtccagCCTGGTCCGGATTCGGTCGGGACTGTTGCCATTTCCCATAGTTGCAATGGAGTGGCAGCACGAGCCTGCAGTCTTGTATCTTTAGAACCTACAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatctgttgatatctatggcaatatgtgaaatattgaaatgttgtgtgttgtagCCTGGTCCGGATTCGGTTGGCATCTTTGCCATTTCGCAAAGATGCAATGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGCTTAGAACCTATGAAG
tgttgat putative branch site (score: 4)
aatatgtgaaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatacgcatctcgtatcattacttaagtgttattttatctgttgatatctatggcaatatgtgaaatattgaaatgttgtgtgttgtagCCTGGTCCGGATTCGGTTGGCATCTTTGCCATTTCGCAAAGATGCAATGGAGTGGCAGCTCGAGCCTGTGGTCTTGTTAGCTTAGAACCTATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC