Sequence
atgc intronic sequence ATGC exonic sequencegtgattatgtattttccatattttccttcattttaatttttgaggctttatatctaaagacacattttataacagGGTGAAGAATACAAGTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G41120.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G41120.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os09g33530.1 (Oryza sativa), 3'ss of exon 10
------------------------------------------------------------------------------------------------gtgattatgtattttccatattt--tccttcattttaatttttgaggctttatatctaaagacacattttataacagGGTGAAGAATACAAGTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAG
| | | || |||| ||||| | | | | | | | || | | || | | ||||| || || || ||||| ||||||||||| || || || ||||| ||||| ||||| | |||||||||| ||| || || |||||||| ||||||||||
gtagcaacagttttggcagatggatcatagagccagtgttatcatgaaatcagtttgaatttggcagatagatcatagagtcagtgataccatgaaatcaatctgaatttggcatatagaacctgtgagatcatgaaatcaatctactgactagaggattggctgttcttcagGGAGAGGAGTATAAGTTGTTTTGGCCAGAGCAGTCTGAATTTGTGAGGATGGCATCAAGGTTTGGAGCAACAATAATACCATTTGGAGTAGTTGGAGAAG
upper sequence: AT5G41120.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA16G05580.1 (Glycine max), 3'ss of exon 10
----------------gtgattatgtat-tttccatattttccttcatttta----atttttgaggcttt----atatctaaagacacattttataacagGGTGAAGAATACAAGTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAG
| | | | | | | || | | | | ||| || ||| | || || || || |||| | ||||||||||||||||||||||| ||||| ||||| || |||||||||||||| ||| | | ||||||||| ||||| | |||||||| || ||||||||||
tatgaaattttttaggctcactttatctgtctctgtctctatttatgctttgaaatataccagagtcgtttaaaatctccaacattgcattaattctcagGGTGAAGAATACAAGTTATTCTGGCCTGAACAATCCGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATAGTACCTTTTGGTGTAGTTGGAGAAG
upper sequence: AT5G41120.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA16G05570.1 (Glycine max), 3'ss of exon 12
-----------gtgattatgtattttccatattttccttcattt-taatttttgaggctttata----tctaaagac----acatttta-taa----cagGGTGAAGAATACAAGTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAG
| || | | | | || |||| | ||| | | || | | |||| | ||||||| ||| ||||||||||||||||||||||| ||||| |||| || |||||||||||||| ||| | | ||||||||| ||||| | |||||||| | ||||||||||
ttggttattttttagacccactttatttgtctctctctgtatttgtgctttgaaatacactagaatagtttaaaatcttcagcattttaataattttcagGGTGAAGAATACAAGTTATTCTGGCCTCAACAATCTGAGTTTGTAAGGATGGCAGCAAGATTTGGAGCCAAAATTGTACCTTTTGGTGCAGTTGGAGAAG
upper sequence: AT5G41120.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv14s0068g01430.t01 (Vitis vinifera), 3'ss of exon 10
------------------------gtgattatgtattttccatatttt--ccttcattttaatttttgaggctttatatctaaagacacattttataacagGGTGAAGAATACAAGTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAG
| ||| | | ||| | | ||||||| | ||| || ||| || | ||||||| ||||||||||| |||||||||||||| || |||||||| | || || ||| |||||||| ||||| || || |||||||||||||||||||
aaaatatgtgtgcatgtatatttcatagccatgaagtagacatgtcggggtcacaattttaaaataccttttgcaatactcaattgttcatattgtt-tagGGTGAGGAATACAAGTTGTTTTGGCCAGAACAATCTGAGTTTGTCCGAATTGCGGCTAGGTTTGGAGCCAAAATTATACCCTTTGGAGTTGTTGGAGAAG
upper sequence: AT5G41120.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv14s0068g01440.t01 (Vitis vinifera), 3'ss of exon 10
-------------------------------------------------------------------------------------------------------------------gtgattatgtattttccatattttccttc--attttaatttttgaggctttatatctaaagac--acattttataa----cagGGTGAAGAATACAAGTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAG
||| | | | | || | |||| |||| || | || | || | | || | || |||| | |||||||| ||||||||||| |||||||||||| || |||||| | | || || ||| ||||||||| ||||| | || ||||| || ||||||||||
gtaacattttagtaattacattctacattgaagtacattgctctggataaaagtgtttttttttttcctttaggttcctacaacaaaaattcatataaacatgtgcattatatgtgtgcatggctgtgaaagaaatatgccttagaatttgaagtattaaactcttttttgcaacacccaactgtttacattgtccagGGTGAGGAATACAAGTTGTTTTGGCCAGAATCATCTGAGTTTATCCGAATGGCGGCTAGATTTGGAGCCAAAATTGTACCCTTTGGGGTGGTTGGAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttccttcattttaatttttgaggctttatatctaaagacacattttataacagGGTGAAGAATACAAGTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAG
atctaaa putative branch site (score: 3)
ttcattttaatttttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattatgtattttccatattttccttcattttaatttttgaggctttatatctaaagacacattttataacagGGTGAAGAATACAAGTTATTTTGGCCAGAACATTCGGAGTTTGTAAGGATAGCATCTAAATTTGGAGCAAAAATCATTCCTTTTGGAGTTGTTGGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA