Sequence
atgc intronic sequence ATGC exonic sequencegtataaaaaaaggttttttttgtatttgttgatgaaagattagggtttttgattgagaaattctgtagCGGCGGTGGCATGGCGTGCTGGTGAGCCATTGGTTATGGAGGAAGTTGAAGTGAGTCCACCTCAACCACTTGAGATCAGAATTAAAGTTGTATGTACATC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G24760.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G24760.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G23820.1 (Glycine max), 3'ss of exon 1
--------------------------------------------------gtataaaaaaaggttttttttgtatttgttg-atgaaagattagggtttttgat---------tgagaaattctgtagCGGCGGTGGCATGGCGTGCTGGTGAGCCATTGGTTATGGAGGAAGTTGAAGTGAGTCCACCTCAACCACTTGAGATCAGAATTAAAGTTGTATGTACATC
|| | | | ||| | | | || || || | || ||||| | || | || ||| || ||||||||| | ||||| || ||||||| || |||||||| ||||||||||| ||||||||| | ||||| || ||||| ||||| | || ||
gtaaagtcagccacccttttcctttttcattttcttgttttgatatctctgtctgtgcattgttttatgatcaacatgggatattaattcgtgtggcttttgttaatggtatgtggaacatggaacagCTGCAGTGGCATGGGGAGCTGGGGAAGCATTGGTGATAGAGGAAGTGGAAGTGAGTCCTCCTCAACCAATGGAGATTAGGATTAAGGTTGTCTCCACTTC
upper sequence: AT5G24760.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G29070.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------gtataaaaaaaggttttttttgtatttgttgatgaaagattagggtttttgat-tgagaaattctgtagCGGCGGTGGCATGGCGTGCTGGTGAGCCATTGGTTATGGAGGAAGTTGAAGTGAGTCCACCTCAACCACTTGAGATCAGAATTAAAGTTGTATGTACATC
| | | | | | |||| || | | || | || || || | || || ||| || ||||||||| | ||||| || ||||||| ||||||||||| ||||||||||| || |||||| | ||||| || ||||| ||||| | || ||
gtaaactcagtcacccttttcctttttcattttcttgttttgatatctctgtctgtccatttttttatgatgaacatgggatattaattcgtatagcttttgttaattgcatgtggaacatggtgcagCTGCAGTGGCATGGAGAGCTGGGGAAGCATTGGTGATGGAGGAAGTAGAAGTGAGTCCTCCCCAACCAATGGAGATTAGGATTAAGGTTGTCTCCACCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttgtatttgttgatgaaagattagggtttttgattgagaaattctgtagCGGCGGTGGCATGGCGTGCTGGTGAGCCATTGGTTATGGAGGAAGTTGAAGTGAGTCCACCTCAACCACTTGAGATCAGAATTAAAGTTGTATGTACATC
ttttgat putative branch site (score: 4)
tttgtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataaaaaaaggttttttttgtatttgttgatgaaagattagggtttttgattgagaaattctgtagCGGCGGTGGCATGGCGTGCTGGTGAGCCATTGGTTATGGAGGAAGTTGAAGTGAGTCCACCTCAACCACTTGAGATCAGAATTAAAGTTGTATGTACATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA