Sequence
atgc intronic sequence ATGC exonic sequencegttagacctctgtcaaaactttggttaccctattttttttgtcttacttcataaacatcttcttaaggatttttcatacttccttcactagACATCAATGAGTGCAAAGAGAAGAAAGCATGTCAGTGCCCGGAATGTAGCTGTAAGAACACCTGGGGAAGCTATGAGTGCTCTTGTAGCGGGGACCTTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G14720.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G14720.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 9
----gttagacctctgtcaaaactttggttaccctattttttttgtcttacttcataaacatc--ttctta-aggatttttcatacttccttcac-----tagACATCAATGAGTGCAAAGAGAAGAAAGCATGTCAGTGCCCGGAATGTAGCTGTAAGAACACCTGGGGAAGCTATGAGTGCTCTTGTAGCGGGGACCTTCT
|| | || || || | ||| | |||| || | | | |||| ||| | |||||| || | | || | || || |||||||||||||||||||||||| ||||| ||||| || || ||||| || || | | || ||||| |||||| || |||| || |||||||| ||
aatcattgtgagtgtggtaatgctgggagtac---aaattttgtgccatgcaacatatacaacagttcttatagtgtaccttattttcaatttacgtttgcagACATCAATGAGTGCAAAGAGAAAAAAGCTTGTCAATGTCCAGAATGCAGTTGCAGAGATACATGGGGTGACTATGAATGTACTTGCAGTGGGGACCTACT
upper sequence: AT2G14720.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G27000.1 (Glycine max), 3'ss of exon 9
gttagacctctgtcaaaactttggttaccc----tattttttttgtcttacttcataaacatcttcttaa-----ggatttttcatacttccttcactagACATCAATGAGTGCAAAGAGAAGAAAGCATGTCAGTGCCCGGAATGTAGCTGTAAGAACACCTGGGGAAGCTATGAGTGCTCTTGTAGCGGGGACCTTCT
||| ||| || | | ||| | | ||| ||| || | |||||| | | || | | | | | |||| |||||| |||| ||||||||||||||||| ||||||||||| ||||||||||| ||||| || |||||||||||||| ||| |||| || ||||| ||| |
attaatcctttgccttggcattgttaattgatgatatctttgaatgttttcatcataactaaaagccaaatatctgaactccttttgcttcacctttcagACATTGATGAATGCAAAGAGAAGAAAGCTTGTCAGTGCCCTGAATGTAGCTGCAAGAATACTTGGGGAAGCTATGACTGCACTTGCAGTGGGGATCTTTT
upper sequence: AT2G14720.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 9
gttagacctctgtcaaaactttggt---------taccct--attttttttgtcttacttcataaacatcttcttaaggatttttcatacttccttcact-agACATCAATGAGTGCAAAGAGAAGAAAGCATGTCAGTGCCCGGAATGTAGCTGTAAGAACACCTGGGGAAGCTATGAGTGCTCTTGTAGCGGGGACCTTCT
|| ||| || | | ||| | |||| | | | |||| || || | | || || | | | ||| | | || | | | |||||| | || ||||||||||||||||| ||||||||||| ||||||||||| ||||| || |||||||||||||| ||| |||| || ||||| ||| |
--taatcctttgccttggcattgttaattgatgatacctttgaatcttttcatcataactaa-aagcaaaatatctgaactcttttttgcctcatcctttcagACATTGACGAATGCAAAGAGAAGAAAGCTTGTCAGTGCCCTGAATGTAGCTGCAAGAATACTTGGGGAAGCTATGACTGCACTTGCAGTGGGGATCTTTT
upper sequence: AT2G14720.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA11G00370.1 (Glycine max), 3'ss of exon 9
----------gttagacctctgtcaaaactttggttaccctattttttttgtcttacttcataaacatcttcttaaggatttttcatacttccttcactagACATCAATGAGTGCAAAGAGAAGAAAGCATGTCAGTGCCCGGAATGTAGCTGTAAGAACACCTGGGGAAGCTATGAGTGCTCTTGTAGCGGGGACCTTCT
|| || | | | ||| | | | | | | | | || | | | | || || | ||| || ||| || |||| |||||||||||||| || ||||||||||| ||||||||||| ||||| || |||||||||||||| ||| |||||| || || |||||
aatctgtgggtttgaacaagtattgcgaacttgatgatacatacctagtgattgttttccacataacaagtgaaactgaacttatgtttcatctttac-agATATTGATGAATGCAAAGAGAAGAAGGCTTGTCAGTGCCCTGAATGTAGCTGCAAGAATACGTGGGGAAGCTATGACTGCAGTTGTAGTGGAGATCTTCT
upper sequence: AT2G14720.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA01G45380.1 (Glycine max), 3'ss of exon 9
---gttagacctctg---tcaaaactttggttaccctattttttttgtct--tacttcataaacatcttcttaaggatttttcatacttccttcac-tagACATCAATGAGTGCAAAGAGAAGAAAGCATGTCAGTGCCCGGAATGTAGCTGTAAGAACACCTGGGGAAGCTATGAGTGCTCTTGTAGCGGGGACCTTCT
| | | || | || ||| || || | | | || | | | | | || | || ||| | | ||| || |||| |||||||||||||| || ||||||||||| || |||||||| ||||| || |||||||||||||| ||| |||||| || || |||||
tcttctcaatccgtgggtttgaagtattgcgaacttgatgatacctagtgaatgttttccacataacacgtgaaattgaacttatgtttcatctatacagATATAGATGAATGCAAAGAGAAGAAGGCTTGTCAGTGCCCTGACTGTAGCTGCAAGAATACTTGGGGAAGCTATGACTGCAGTTGTAGTGGAGATCTTCT
upper sequence: AT2G14720.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 9
--------gttagacctctgtcaaaactttggttac-cctattttttttgtcttac-ttcataaacatcttcttaaggatttttcatacttccttcactagACATCAATGAGTGCAAAGAGAAGAAAGCATGTCAGTGCCCGGAATGTAGCTGTAAGAACACCTGGGGAAGCTATGAGTGCTCTTGTAGCGGGGACCTTCT
||| | ||| ||| | | | | || || || | | | || ||| | | | | ||| | | || ||| | |||| |||||||| |||||||| ||||||||||| ||||| ||||| || ||||| ||||| ||||| |||||| |||| || ||||| ||| |
tattttcagttgaaagcatgttaaagagaagtcaaaatttgtgaacagaatcctaagttgacattgctgtttttatgtaactgtttctcttaccttac-agATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCTGCAAAAACACATGGGGTAGCTACGAGTGCACTTGCAGTGGGGATCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgtcttacttcataaacatcttcttaaggatttttcatacttccttcactagACATCAATGAGTGCAAAGAGAAGAAAGCATGTCAGTGCCCGGAATGTAGCTGTAAGAACACCTGGGGAAGCTATGAGTGCTCTTGTAGCGGGGACCTTCT
gtcttac putative branch site (score: 3)
tttttcatacttcctt putative PPT
atttttcata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagacctctgtcaaaactttggttaccctattttttttgtcttacttcataaacatcttcttaaggatttttcatacttccttcactagACATCAATGAGTGCAAAGAGAAGAAAGCATGTCAGTGCCCGGAATGTAGCTGTAAGAACACCTGGGGAAGCTATGAGTGCTCTTGTAGCGGGGACCTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC