Sequence
atgc intronic sequence ATGC exonic sequencegttggttcccaaaattgttcctgcctagaccttcttaaaagctaagttatatagtatgatgtgatcctttttatttgatctccatgcgtcttgtggctatgtttctcttttagATTCCAAGGAAGTTTACGAGTAAAGTTGAAGGGAAGATGAGTTATGAAGATTTTGTGTACTTCATTCTCGCTGAGGAAGACAAGTCTTCCGAGCCTAGTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03960.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03960.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 8
gttggttcccaaaattgttcctgcctagaccttcttaaaagctaagttatatagtatgatgtgatcct-ttttatttgatctccatgcgtcttgtggctatgtttctcttttagATTCCAAGGAAGTTTACGAGTAAAGTTGAAGGGAAGATGAGTTATGAAGATTTTGTGTACTTCATTCTCGCTGAGGAAGACAAGTCTTCCGAGCCTAGTC
|| || ||| | ||| || ||| || ||| ||| || ||| || |||||| || ||| | ||||| || || || || | ||||| |||||| |||||||||||||||| ||||| ||| | ||||||||||||| || ||||||||||| |
------------------------------gttagtatgttctattctgcatacagaactgagatgctgccttagttggcctaaatgttgtttccta-tatgttact----tagGTCCCAAGAAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGATTTTGTTTACTTTATTTTGTCTGAGGAAGACAAATCATCCGAGCCTAGCC
upper sequence: AT1G03960.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 9
-----------------gttggttcccaaaatt---gttcctgcctagaccttcttaaaagct-aagttatatagtatgatgtgatcctttttatttgatctccatgcgtcttgtggctatgtttctcttttagATTCCAAGGAAGTTTACGAGTAAAGTTGAAGGGAAGATGAGTTATGAAGATTTTGTGTACTTCATTCTCGCTGAGGAAGACAAGTCTTCCGAGCCTAGTC
| |||| ||| | | | | | || ||| |||| ||| | || |||| | || |||| | | || | | ||||| | || | | || ||||||| |||||||| || || |||| ||||||||| |||||||||||||||| |||||||| || | ||||| || ||||| || |||||| |||
gtttgcttttatcttggaatatttccaaaagattcagattaaattaataactgctttaaagtagaagcaacatgctatg-taaaatgactttt--tccaccttttggttttttgtgcttcaattatcttctcagGTTCCAAGAAAGTTTACTAGCAAGATTGAGGGGAAGATGGGTTATGAAGATTTTGTTTACTTCATGCTGTCAGAGGAGGATAAGTCATCAGAGCCTGGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtgatcctttttatttgatctccatgcgtcttgtggctatgtttctcttttagATTCCAAGGAAGTTTACGAGTAAAGTTGAAGGGAAGATGAGTTATGAAGATTTTGTGTACTTCATTCTCGCTGAGGAAGACAAGTCTTCCGAGCCTAGTC
atttgat putative branch site (score: 5)
ctatgtttctctttt putative PPT
tttttatttgatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggttcccaaaattgttcctgcctagaccttcttaaaagctaagttatatagtatgatgtgatcctttttatttgatctccatgcgtcttgtggctatgtttctcttttagATTCCAAGGAAGTTTACGAGTAAAGTTGAAGGGAAGATGAGTTATGAAGATTTTGTGTACTTCATTCTCGCTGAGGAAGACAAGTCTTCCGAGCCTAGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA