Sequence
atgc intronic sequence ATGC exonic sequence...catatctaacatttacaattacactacataaatatggatgatatatgtctttggcaaatcgtggtagctaatgtgcaaaaacttgggttttaacgaacagGCGGCAGCGATAAGGCTGGAGATAAGAGGAGGAGACTGGAAAGATGCGTTTATGCAAATGGATGGAGAGCCATGGAAACAGCCTATGACCAGAGACTACT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57690.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57690.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G30040.1 (Glycine max), 3'ss of exon 4
catatctaacattta-caattacactacataaatatggatgatatatgtctttggcaaatcgtggtagctaatgtgcaaaaacttgggttttaacgaacagGCGGCAGCGATAAGGCTGGAGATAAGAGGAGGAGACTGGAAAGATGCGTTTATGCAAATGGATGGAGAGCCATGGAAACAGCCTATGACCAGAGACTACT
| ||||||| | || || | || | | || || || ||| | ||||| | | | | | | ||| |||| |||| || | |||| | ||||| || || ||||||||||| |||||||||||||||||||| || |||||||| ||||||| || |||| ||
gtttgctaacatgaatcagttttctttgattttgttctaattggtaactcattagcatcttttggtatgtgtaaaattgactatagaggtctaattt-tagGCAACAGCTATTCGATTGGAAGTTAGAGGTGGGGAATGGAAAGATGCATTTATGCAAATGGATGGAGAACCCTGGAAACAACCTATGAGCAAGGACTTCT
upper sequence: AT5G57690.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G22370.1 (Glycine max), 3'ss of exon 4
--catatctaacatttacaattacactacataaatatggatgatatatgtctttggcaaatcgtggtagctaatgtgcaaaaacttgggttttaacgaacagGCGGCAGCGATAAGGCTGGAGATAAGAGGAGGAGACTGGAAAGATGCGTTTATGCAAATGGATGGAGAGCCATGGAAACAGCCTATGACCAGAGACTACT
| | | | | || |||| | |||||||| | || | || || ||| ||| | | || | | | | ||| |||| |||| || | |||| | ||||| || || ||||||||||| |||||||||||||||||||| || |||||||| || |||| || |||| ||
aactttgatcagaactattattattgt-tataaatatatacgactgttatcattagcatcatttggcatgtgtgaaattgaatgtagaggtctaattt-tagGCAACAGCTATTCGATTGGAAGTCAGAGGTGGTGAATGGAAAGATGCATTTATGCAAATGGATGGAGAACCGTGGAAACAACCAATGAGCAAGGACTTCT
upper sequence: AT5G57690.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G01360.2 (Glycine max), 3'ss of exon 11
catatctaacatttacaattacactacataaatatggatgatatatgtctttggcaaatcgtggtagctaatgtgcaaaaacttgggtttta---acgaa-----cagGCGGCAGCGATAAGGCTGGAGATAAGAGGAGGAGACTGGAAAGATGCGTTTATGCAAATGGATGGAGAGCCATGGAAACAGCCTATGACCAGAGACTACT
| | ||| || || | ||| | | | | | || || | | || | | | | | | |||| ||| | | || ||||| |||| || | |||| | ||||| ||| | |||||| | || | |||||||||||||||||| || ||||||||||| ||| || |||| ||
----ctttatattgcca--taatttgcatcgtcaaaatttgtctttctcaatgaccagtcccactggtt--tctcttgactcttgagttctgtttataaatctttcagGCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTATATGCAAATGGATGGAGAACCCTGGAAACAGCCATTGAGCAAGGACTTCT
upper sequence: AT5G57690.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 11
catatctaacatttacaattacactac-ataaatatggatgatatatgtctttggcaa-atcgtggtagctaatgtgcaaaaacttgggttttaacgaacagGCGGCAGCGATAAGGCTGGAGATAAGAGGAGGAGACTGGAAAGATGCGTTTATGCAAATGGATGGAGAGCCATGGAAACAGCCTATGACCAGAGACTACT
|| ||| || | || | | | || || |||| | || | | | || | || | || || || | ||||| ||||| || | |||| || ||||| ||||| ||||| | || | |||||| |||||||| ||||||||||||||||| || | || || | |
--gatttaagtgtttccatcatagtgttattgatgctgatgttggattctgaaatctatgcttttataattccattgaataagttttatgggtatctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATATATGCAGATGGATGGGGAGCCATGGAAACAGCCAATAAACAATGAGTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtctttggcaaatcgtggtagctaatgtgcaaaaacttgggttttaacgaacagGCGGCAGCGATAAGGCTGGAGATAAGAGGAGGAGACTGGAAAGATGCGTTTATGCAAATGGATGGAGAGCCATGGAAACAGCCTATGACCAGAGACTACT
ttttaac putative branch site (score: 2)
aaaaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catatctaacatttacaattacactacataaatatggatgatatatgtctttggcaaatcgtggtagctaatgtgcaaaaacttgggttttaacgaacagGCGGCAGCGATAAGGCTGGAGATAAGAGGAGGAGACTGGAAAGATGCGTTTATGCAAATGGATGGAGAGCCATGGAAACAGCCTATGACCAGAGACTACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - -ctaacat
- - - - - - - - - - - - -acataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaaac