Sequence
atgc intronic sequence ATGC exonic sequencegtgtgcccacctttcttaggcagatttaaatcgccttttatcctcaaactcagatttgtttgtcttgcaattagGACGATAGAGAACTTAAGCGACAGAGACGGAAGCAGTCCAATAGGGAGTCTGCTCGAAGATCAAGGTTGCGTAAACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35530.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os12g13170.1 (Oryza sativa), 3'ss of exon 10
------------gtgtgcccacctttcttaggcagat-ttaaatcgccttttatcct--caaactcagat----------ttgtttgtcttgcaatt-agGACGATAGAGAACTTAAGCGACAGAGACGGAAGCAGTCCAATAGGGAGTCTGCTCGAAGATCAAGGTTGCGTAAACAG
| | | | | || | | || | | || | || |||| ||| ||| | || ||| |||| || | ||||| || | |||||| | || || ||||| |||||||||||||| ||||| ||||||||||| |||
atggcacttaatcatcaacaatcctatggatacaaacatgaagttttcagtttttctggcaaatggagaaattagtcgtgttgactctcccatgattcagGATGAACGGGAACTCAAAAGGCAGAGAAGAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAG
upper sequence: AT2G35530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G088140_T01 (Zea mays), 3'ss of exon 9
---------------gtgtgcccacctttcttaggcagatttaaatcgccttt--------tatcctca--aactcagatttgtttgtcttgcaatt-agGACGATAGAGAACTTAAGCGACAGAGACGGAAGCAGTCCAATAGGGAGTCTGCTCGAAGATCAAGGTTGCGTAAACAG
|||| || | | | || | || || || ||| | ||| | || |||| || |||| || ||||| || || ||| | ||||||||||||||||||||||| || ||||| ||||| |||||||||
ttgacactagagaaattgtgtatacaaattcaacatatatcaatatggcaattggagaagctattcatgttgactgtagtgggtactacttgtggttcagGATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG
upper sequence: AT2G35530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G074373_T02 (Zea mays), 3'ss of exon 11
--------------------------gtgtgcccacctttcttaggcagatttaaatcgccttttatcctcaaactcagatttgtttgtcttgcaatt-agGACGATAGAGAACTTAAGCGACAGAGACGGAAGCAGTCCAATAGGGAGTCTGCTCGAAGATCAAGGTTGCGTAAACAG
|||| || | | | | || | | || | | ||| || || ||||| || |||| || | ||||| || | || | | | || ||||| |||||||||||||| || ||||| |||||||||||||||
tagagattgaattgacactagagaaattgtggatacaaatttaacatatatcaatctggcaatcggagaagctattcatgttgactt-tcttgtggttcagGATGAACGTGAACTCAAAAGGCAAAAAAGAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagatttaaatcgccttttatcctcaaactcagatttgtttgtcttgcaattagGACGATAGAGAACTTAAGCGACAGAGACGGAAGCAGTCCAATAGGGAGTCTGCTCGAAGATCAAGGTTGCGTAAACAG
tttgtctt CT-rich tract
tttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgcccacctttcttaggcagatttaaatcgccttttatcctcaaactcagatttgtttgtcttgcaattagGACGATAGAGAACTTAAGCGACAGAGACGGAAGCAGTCCAATAGGGAGTCTGCTCGAAGATCAAGGTTGCGTAAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA