Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttcaggtctcagctgcatttatctttcaaataagttgtttcacataccagtggcttctttcatctcctctaactatattgattattattttgtagACTGGTTTGACGGACTCAATACTTTCATGAGGTATATTTGCCATAAGAGTTGGTTAGGCGGCTGGCTAATGCCCCAGAAGAAAAGCTATTTTGCCCTGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G11800.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA14G08860.1 (Glycine max), 3'ss of exon 8
gtgagtttcaggtctcagctgcatttatctttcaaataagttgtt-tcacataccagtggct---tctttcatctcctctaactatattgattattat-tttgtagACTGGTTTGACGGACTCAATACTTTCATGAGGTATATTTGCCATAAGAGTTGGTTAGGCGGCTGGCTAATGCCCCAGAAGAAAAGCTATTTTGCCCTGCA
|| |||| | | ||| ||| | | || | ||| || || | || |||| || ||||| || | || |||||||||||| |||||| | || || ||||||||||| ||||||| || |||||||| || ||||| |||||||||||||| || |||||||| ||||
------ttttggtcatcttacctcatctctatcagaaagtttaaaattgaatatttatgcctaacacaaatatggttactaattaatatgattgttttcttcacagACTGGTTTGATGGACTCCAGACCTTTATGAGGTATATATGCCATAGAAGCTGGTTAGGTGGATGGCTCATGCCCCAGAAGAAGAGTTATTTTGCTTTGCA
upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G36310.1 (Glycine max), 3'ss of exon 8
gtgagtttcaggtctcagctgcatttatctttcaaataagttgtttcacataccagtggcttctttcatctcctctaactatattgattattat-tttgtagACTGGTTTGACGGACTCAATACTTTCATGAGGTATATTTGCCATAAGAGTTGGTTAGGCGGCTGGCTAATGCCCCAGAAGAAAAGCTATTTTGCCCTGCA
|| | |||| || ||| | ||| ||| | | || || || || |||| || | |||||| | || |||||||||||| |||||| | || || ||||||||||| || |||| || |||||||| || ||||| |||||||||||||| || |||||||| ||||
-tggtcattttacctcatctaacttttttttttaaa-atttaaaactgtgtatttatgcctaacactatggttactaattaatataattattttcttcacagACTGGTTTGATGGACTCCAGACCTTTATGAGGTATATATGTCATAGAAGCTGGTTAGGTGGATGGCTCATGCCCCAGAAGAAGAGTTATTTTGCTTTGCA
upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 9
--------gtgagtttcaggtctcagctgcatttatctttcaaataagttgtttcacataccagtggcttctttcatctcctctaactatattgattattattttgtagACTGGTTTGACGGACTCAATACTTTCATGAGGTATATTTGCCATAAGAGTTGGTTAGGCGGCTGGCTAATGCCCCAGAAGAAAAGCTATTTTGCCCTGCA
|| | | |||||| | | |||| || || || || || | || | || | | | | | | ||| | || || |||| ||| |||||||| ||||| | |||||||||||||| || || |||||||| |||||||| || ||| | ||||| |||||||| || |||||||| ||||
ttttgttagtaaatctcaggtttttatt-cattaataagtcct-caatttcctttgccta--gatagcatatcac-tatggttcaacaa----aatgtttcttttacagATTGGTTTGATGGACTTCACACTTTCATGAGGTACATATGTCATAAGAGCTGGTTAGGTGGGTGGTTTATGCCTCAGAAGAAGAGTTATTTTGCTTTGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacataccagtggcttctttcatctcctctaactatattgattattattttgtagACTGGTTTGACGGACTCAATACTTTCATGAGGTATATTTGCCATAAGAGTTGGTTAGGCGGCTGGCTAATGCCCCAGAAGAAAAGCTATTTTGCCCTGCA
ttatttt CT-rich tract
tctaactatattgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttcaggtctcagctgcatttatctttcaaataagttgtttcacataccagtggcttctttcatctcctctaactatattgattattattttgtagACTGGTTTGACGGACTCAATACTTTCATGAGGTATATTTGCCATAAGAGTTGGTTAGGCGGCTGGCTAATGCCCCAGAAGAAAAGCTATTTTGCCCTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA