Sequence
atgc intronic sequence ATGC exonic sequencegtgatgtatccattttccatctcttgtttttccttttctctttttttttttttgggtgtatatggaaaactcaatgcaataaataacttgtttcagGGAGAAGATTTTAAGAAAGAAAATTTGCGGTACCATAAGATAATCATCTTAACAGATGCAGATGTTGATGGTGCACATATCCGGACACTTCTGTTGACCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04130.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04130.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 16
gtgatgtatccattttccatctcttgtttttccttttctctttttttttttttgggtgtata-tggaaaactcaatgcaataaataacttgtttcagGGAGAAGATTTTAAGAAAGAAAATTTGCGGTACCATAAGATAATCATCTTAACAGATGCAGATGTTGATGGTGCACATATCCGGACACTTCTGTTGACCT
| | | |||| | | | || || | | |||| || |||||||| || |||||||| || ||| | | || || ||||||||| |||| | || ||||| ||||| |||||||||||||||||||| ||||| | || |
----------------------------------gtgcatactgttttgatctaaacttctactgttattgttttcttctctaatattttctttcagGGCGAGGATTTTAACAAGGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTT
upper sequence: AT5G04130.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA19G31030.1 (Glycine max), 3'ss of exon 16
gtgatgtatccattttccatctcttgtttttccttttctctttttttttttttgggtgtatatggaaaactcaatgcaataaataactt-----gtttcagGGAGAAGATTTTAAGAAAGAAAATTTGCGGTACCATAAGATAATCATCTTAACAGATGCAGATGTTGATGGTGCACATATCCGGACACTTCTGTTGACCT
| |||| | | |||| | | | | | ||| | | | || ||| | ||| | |||| ||| |||||||||||| |||||||||||||| | || || |||||||| || || || || ||||| ||||| |||||||| || ||||| ||||| || |||| |
caattatatcagagtaaaaatccttgatcacctgtgccagaatcctttgctcttaactaacataaaaattttaat-taggaaattccttttgttgtttcagGGAGAGGATTTTAAGAAAGATGCACTCCGATATCATAAGATTATTATTTTGACTGATGCTGATGTGGATGGTGCCCACATCCGAACACTGCTACTGACAT
upper sequence: AT5G04130.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv08s0007g05120.t01 (Vitis vinifera), 3'ss of exon 16
gtgatgtatccattttccatctctt--gtttttccttttctctttttttttttttgggtgtatatggaaaactcaatgcaataaataacttgtttcagGGAGAAGATTTTAAGAAAGAAAATTTGCGGTACCATAAGATAATCATCTTAACAGATGCAGATGTTGATGGTGCACATATCCGGACACTTCTGTTGACCT
| | |||||| | ||| |||||| |||| | || ||||||| || || | | | | || | || | || ||||||||| || |||||||| || ||| | | || || ||||| || ||||||||||||||||| ||||| |||||||| |||||||| || || |||||||| |
---gttaactcattttttgttccttaggtttttgtttttgttttctttttttatttttggtgaacagtacagcttattc--tatcttcctggtttcagGGGGAGGATTTTAAAAAGGAAGCTCTCCGTTATCATAAAATCATCATCTTAACAGATGCTGATGTGGATGGTGCTCATATCCGAACTCTGCTGTTGACTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttttttgggtgtatatggaaaactcaatgcaataaataacttgtttcagGGAGAAGATTTTAAGAAAGAAAATTTGCGGTACCATAAGATAATCATCTTAACAGATGCAGATGTTGATGGTGCACATATCCGGACACTTCTGTTGACCT
aaataac putative branch site (score: 2)
cttgtttc CT-rich tract
aataaataacttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatgtatccattttccatctcttgtttttccttttctctttttttttttttgggtgtatatggaaaactcaatgcaataaataacttgtttcagGGAGAAGATTTTAAGAAAGAAAATTTGCGGTACCATAAGATAATCATCTTAACAGATGCAGATGTTGATGGTGCACATATCCGGACACTTCTGTTGACCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG