Sequence
atgc intronic sequence ATGC exonic sequencegtaacacaacgtctttactattgtaataaaatattctaaggtaacataacggtttatgtttattagcaaattaaatgtaaattttctctctgctataaaatttccaaaattcattagatgtatcatgatcgtaatttttacaagacaatttgataatgaaaattttaaaaataattagGGAGTTCAAAGAGAAAAACAAAGTGGATAAAGTGGTGGTACTGTGGACGGCAAACACAGAAAGATACAGCAATGTGGTGGTTGGTCTTAACGACACGACG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10170.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
gtaacacaacgtctttactattgtaataaaatattctaaggtaacataacggtttatgtttattagcaaattaaatgtaaattttctctctgctataaaatttccaaaattcattagatgtatcatgatcgtaatttttacaagacaatttg-ataatgaaaattttaaaaat-aattagGGAGTTCAAAGAGAAAAACAAAGTGGATAAAGTGGTGGTACTGTGGACGGCAAACACAGAAAGATACAGCAATGTGGTGGTTGGTCTTAACGACACGACG
| || | ||||| ||| || || | | ||| | | | | || ||| | || || ||||| | | || |||||||||||| || || | ||||||||| || |||||||| ||||||| |||||||| ||||| ||||||||||| ||||| || || ||||| | |
-------------------------------------------------------------------------------tagttccagtctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaa-acattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g22450.1 (Oryza sativa), 3'ss of exon 4
gtaacacaacgtctttactattgtaataaaatattctaaggtaacataacggtttatgtttattagcaaattaaatgtaaattttctctctgctataaaatttccaaaattcattagatgtat-catgatcgtaatttttacaagacaatttgataatgaaaattttaaaaataattagGGAGTTCAAAGAGAAAAACAAAGTGGATAAAGTGGTGGTACTGTGGACGGCAAACACAGAAAGATACAGCAATGTGGTGGTTGGTCTTAACGACACGACG
||| | |||||| | || || || | ||||||||| | | || | ||| | | | |||| | || | | || || ||||||||||| ||||| | ||| ||||| || |||||||| ||||||||||| ||||| || | |||||||| ||||||| || | |||||||| | |
---------------------------------------------------------------------------tgtga-ttttctgtttgacatgaa-ctgacaaaattcagcaaaagtttgtatgtacattaattttg--gttttgatggacatgggtgggatttgttggtataagGGAGTTCAAGGAGAAGAGCAAGGTGGACAAGGTGGTGGTGCTGTGGACGGCCAACACGGAGCGGTACAGCAACGTGGTGGCCGGGATGAACGACACCATG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 4
gtaacacaacgtctttactattgtaataaaatattctaaggtaacataacggtttatgtttattagcaaattaaatgtaaattttctctctgctataaaatttccaaaattcattagatgtatcatgatcgtaatttttacaagacaatttgataatgaaaattttaaaaataattagGGAGTTCAAAGAGAAAAACAAAGTGGATAAAGTGGTGGTACTGTGGACGGCAAACACAGAAAGATACAGCAATGTGGTGGTTGGTCTTAACGACACGACG
| || ||| ||| || || | | | | | |||||| | ||| | || | | | | || || |||||||| || ||||| ||||||||||| || || || || |||||||| |||||||| ||||| ||||||||||| | |||||| |||||||| | |
----------------------------------------------------------------------------atggtttggggatctagattaacatgattgaagcaacatggctcactggtatacgtaatccattatagaagctatggc--ttatatgtagccaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGCAAACACTGAAAGGTACAGCAATGTATGTGCTGGTCTCAACGACACAATG
upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 4
gtaacacaacgtctttactattgtaataaaatattctaaggtaacataacggtttatgtttattagcaaattaaatgtaaattttctctctgctataaaatttccaaaattcattagatgtatcatgatcgtaatttttacaagacaatttgataatgaaaattt-taaaaataattagGGAGTTCAAAGAGAAAAACAAAGTGGATAAAGTGGTGGTACTGTGGACGGCAAACACAGAAAGATACAGCAATGTGGTGGTTGGTCTTAACGACACGACG
| || || | ||| | | ||| ||| | | || | | | | | | | | ||| || || ||||||||||| || ||| || ||| |||||||| |||||||| |||||||| || |||||||| ||||||| ||| || | || || || || ||||| |
----------------------------------------------------------------------------------------gtagtcgta--atcttcaatttcttaaacatgaatcttaa----aaatggaatgggcttttcttcttttctgattttgtatgtatgattagGGAGTTTAAGGAGGCAACCAAGGTGGATAAGGTGGTGGTGCTGTGGACTGCCAACACAGAGCGATACAGTAATTTGATTGTGGGACTGAATGACACCATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgatcgtaatttttacaagacaatttgataatgaaaattttaaaaataattagGGAGTTCAAAGAGAAAAACAAAGTGGATAAAGTGGTGGTACTGTGGACGGCAAACACAGAAAGATACAGCAATGTGGTGGTTGGTCTTAACGACACGACG
atttgat putative branch site (score: 5)
taatttttacaagaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacacaacgtctttactattgtaataaaatattctaaggtaacataacggtttatgtttattagcaaattaaatgtaaattttctctctgctataaaatttccaaaattcattagatgtatcatgatcgtaatttttacaagacaatttgataatgaaaattttaaaaataattagGGAGTTCAAAGAGAAAAACAAAGTGGATAAAGTGGTGGTACTGTGGACGGCAAACACAGAAAGATACAGCAATGTGGTGGTTGGTCTTAACGACACGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG