Sequence
atgc intronic sequence ATGC exonic sequencegttatgtcccaattattctttcatgtttcttgtttcattaccacaacaacaacatatctcatgtttcttgtttcttttgtggatatacagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51300.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 2
----------gttatgtcccaattattctttcatgtttcttgtttcattaccacaacaacaacatatc--tcatgtttcttgtttcttttgtggatatacagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG
||| | | || || || | |||| || ||| || | || | |||| | | | ||| | | | | | | | | ||||||||||||||| || ||||| || ||||||||||| ||||| || || ||||| |||| ||||||||| || |||||||| ||||| |
gtctcattttgtt-tattataaagtttggttaacgtttttt-ttttataaacattaggttaacaatttgataacgttgtatttgttgtgtatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
upper sequence: AT3G51300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 1
-----gttatgtcccaattattctttcatgtttcttgtttcattaccacaacaacaacatatctcatgtttct-----tgtttcttttgtggatatacagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG
||| | | | ||| | | || || | | ||| | | || || | ||| | | || ||||| | | ||||||||||||| || |||||||| |||||||| || ||||| || || |||||| |||||| ||||| ||||| ||||||||||| |
attgtgtttcatgctatatatgatattatcttataaatatgtttattgataaagaaaaatgatcattatttttgcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
upper sequence: AT3G51300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 1
-gttatgtcccaat------tattctttcatgtttcttgtttcattaccacaacaacaacatatctcatgttt---cttgtttcttttgtggatatacagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG
|| ||| |||| ||| | || | || | | ||| | | || ||| | | ||| | || ||||| | | ||||||||||||| || |||||||| |||||||| || ||||| || || |||||| |||||| ||||| ||||| ||||||||||| |
aattgtgtttcaatgctatatatgatatcctcttataaatatgcttattgagaaagaaagataattttttttttcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
upper sequence: AT3G51300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G36880.4 (Glycine max), 3'ss of exon 1
-gttatgtcccaattattct--ttcatgtttcttgtttcattaccacaacaacaacatatctca-tgtttctt---gtttcttttgtggat----atacagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG
|||| | | | | | || | |||| |||||| || || | | | | | | ||| | ||| ||||| || | ||||||||||||||| || ||||| || |||||||| || ||||| || || ||||| |||| ||||||||| || |||||||| ||||| |
tattatttattatgaagtttggttaacgttttttgttttgtt-ttgtaatgagcatttggttaactatttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
upper sequence: AT3G51300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G36880.2 (Glycine max), 3'ss of exon 2
-gttatgtcccaattattct--ttcatgtttcttgtttcattaccacaacaacaacatatctca-tgtt---tcttgtttcttttgtggatata----cagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG------------
|||| | | | | | || | |||| |||||| || || | | | | | | || | ||| ||||| || || |||||||||||||| || ||||| || |||||||| || ||||| || || ||||| |||| ||||||||| || |||||||| ||||| |
tattatttattatgaagtttggttaacgttttttgttttgtt-ttgtaatgagcatttggttaactatttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGGTAATGCTGCGT
upper sequence: AT3G51300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
---------gttatgtcccaattattctttcatgtttcttgtttcattaccacaacaa-caacatatctcatgtttcttgtttcttttgtggatatacagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG
|| ||||| | | | || ||| || | | | ||| | | ||||| | ||| || | | | ||||||||||||||| || |||||||| ||||||||||| ||||| || || ||||| |||||| || ||||| |||||||| ||||| |
gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttgataggcaaaggacttattgttttatttttgaattattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattaccacaacaacaacatatctcatgtttcttgtttcttttgtggatatacagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG
tttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatgtcccaattattctttcatgtttcttgtttcattaccacaacaacaacatatctcatgtttcttgtttcttttgtggatatacagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG