Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcttttttattttggttcatggttaaaagattgtaagtcttctcttacttgggatctttgcggttatgttctctaaacttactcagATACCTGAAGATCTGCACTTTGTTCTTCGGATGAGGCACACGTTTGAATCACTTGGCTACCAATCCGGATTTTACCTCTCTCAGCTCTTCTCCTCAAACC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15240.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15240.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os11g25920.1 (Oryza sativa), 3'ss of exon 6
----gtaagtcttttttattttggttcatggttaaaagattgtaagtcttct----cttacttgggatctttgcggt---tatgttctctaaacttactcagATACCTGAAGATCTGCACTTTGTTCTTCGGATGAGGCACACGTTTGAATCACTTGGCTACCAATCCGGATTTTACCTCTCTCAGCTCTTCTCCTCAAACC
|| ||| | ||||| | | | | | || | ||| | | | || || || | |||| | |||||||| || || |||||||| || || |||||| |||||| ||| || || || |||||||| || || || | |||||| |||||||||||||| |
cttgacttgtttttgtcgcgttggtcaaagacgccgacgtggacgtgtttgtggggggcactagctaattgggcaaaacgtacgtacgctaa--ctgtgcagATACCGGAGGACCTGCACTTCGTGCTGCGGATGCGGCACATGTTCGAGTCGCTCGGCTACCAGTCGGGCTTCTTCCTCTCCCAGCTCTTCTCCTCCTCGC
upper sequence: AT3G15240.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------------------------------------------------------gtaagtcttttttattttggttcatggttaaaagattgtaagtcttctcttacttgggatctttgcggtt--atgttctctaaact-tactcagATACCTGAAGATCTGCACTTTGTTCTTCGGATGAGGCACACGTTTGAATCACTTGGCTACCAATCCGGATTTTACCTCTCTCAGCTCTTCTCCTCAAACC
||| || | || | || | | || ||| | | || | ||| || || | | || | |||||| ||||||||||| | ||||| ||| | ||||| ||||| |||||||| |||||||||||||| || || ||||||||||| |||||||| ||||
gtgagttaattaattagtaccactttttctctccctccccaaaagccatttttactcattttaagtttacttatttgatatgttaattttaaaagttacattcactagttttaaacagttgttatagctattcattggatggaagaatctgccacaaaaaaatatcaaatgtttgatattttttgttctattttcagATTCCTGAAGATCTCCGTTTTGTGCTTAGAATGAGACACACTTTTGAATCCCTTGGCTACCAATCTGGTTTCTACCTCTCTCAACTCTTCTCTTCAACAA
upper sequence: AT3G15240.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G35490.2 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------------gtaagtc---ttttttattttggttcatggttaaaagattgtaagtcttctcttacttgggatctttgcggttatgttctctaaact-tactcagATACCTGAAGATCTGCACTTTGTTCTTCGGATGAGGCACACGTTTGAATCACTTGGCTACCAATCCGGATTTTACCTCTCTCAGCTCTTCTCCTCAAACC
||| | || ||| || || || | |||| | | | | | || | || || | || | |||||| |||||||| || || ||||| ||| | ||| | ||||| |||||||| |||||||||||||| || || ||||||||||| |||||||| ||||
gtgagttaattaatatgtatcactttttctcctccaaaaaatcatttttactcattttaagtttacttatttgacatggtaattttaagagttacatccgctagttttgtacagtttttatagatattgattggatattagaatctgacacaaagtttgatatttttggttctattttcagATTCCTGAAGACCTCCATTTTGTGCTTAGAATGCGACACACTTTTGAATCCCTTGGCTACCAATCTGGTTTCTACCTCTCTCAACTCTTCTCTTCAACAA
upper sequence: AT3G15240.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 6
---gtaagtcttttttattttggttcatggt-taaaagattgtaagtcttctcttac-------ttgggatctttgcggttatgttctctaaacttactcagATACCTGAAGATCTGCACTTTGTTCTTCGGATGAGGCACACGTTTGAATCACTTGGCTACCAATCCGGATTTTACCTCTCTCAGCTCTTCTCCTCAAACC
||| || || ||||| | ||| || | || | || || | | || | || ||| || | || ||| || ||||||| |||||||| || || ||||| || | ||||||||||| |||||||| || ||||| ||||| || || |||||||| || |||||||| ||||
ctagtatgttgttaatatttctctcggtgggatacatgaatctat-tccacaccaacaaaaacatcaaaatgcttgatatttttttttcttctgtt-ctcagATCCCTGAAGACCTCCATTTTGTGCTAAGAATGAGGCACACTTTTGAATCTCTAGGCTATCAATCAGGGTTCTACCTCTCCCAACTCTTCTCTTCAACAA
upper sequence: AT3G15240.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------------------gtaagtcttttttattttggttcatggttaaaagattgtaagtcttctcttacttgggatct-ttgcggttatgttctctaaacttactcagATACCTGAAGATCTGCACTTTGTTCTTCGGATGAGGCACACGTTTGAATCACTTGGCTACCAATCCGGATTTTACCTCTCTCAGCTCTTCTCCTCAAACC
| | |||| ||| ||| || | | | | | || ||| || |||| | ||| | || || | |||||||||| ||||| || || ||||| || | ||| |||| || |||||||| ||||| || ||||| || || |||||||| ||||||||||| ||||
gtgagtttcatttgtttttgtgctttgatcatctcttgtcctgctagtaattcttgatatttttcagattttgttgatatatgtatgcgtttgagcctttgtttccttgaaaggagttgatctcattgagattatgtatgctcagATACCGGAAGACCTTCATTTTGTGCTGAGAATGCGGCATACCTTTGAATCTCTTGGGTATCAATCTGGGTTCTACCTCTCCCAGCTCTTCTCTTCAACTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaagtcttctcttacttgggatctttgcggttatgttctctaaacttactcagATACCTGAAGATCTGCACTTTGTTCTTCGGATGAGGCACACGTTTGAATCACTTGGCTACCAATCCGGATTTTACCTCTCTCAGCTCTTCTCCTCAAACC
aacttac putative branch site (score: 2)
cttactc CT-rich tract
taaactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcttttttattttggttcatggttaaaagattgtaagtcttctcttacttgggatctttgcggttatgttctctaaacttactcagATACCTGAAGATCTGCACTTTGTTCTTCGGATGAGGCACACGTTTGAATCACTTGGCTACCAATCCGGATTTTACCTCTCTCAGCTCTTCTCCTCAAACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC