Sequence
atgc intronic sequence ATGC exonic sequence...ttttagtccttttattcgcgaggagctggatgagaagaaactctcacgttcagttctgtagtagagatggaatttctaatttagaaccatcaactataacCCAAAAAGAACCAGATTTCGTAAACAACATCGAGGAAGACTAAAAGGAATATCTTCTCGTGGGAATCGTATTTGTTTTGGCAGATATGCTCTTCAAACAC
Basic information
species | Arabidopsis thaliana |
transcript | ATCG00790.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: ATCG00790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os04g16826.1 (Oryza sativa), 3'ss of exon 1
---ttttagtccttttattcgcgaggagctggatgagaagaaactctcacgttcagttctgtagtagagatggaatttctaatttagaaccatcaactataacCCAAAAAGAACCAGATTTCGTAAACAACATCGAGGAAGACTAAAAGGAATATCTTCTCGTGGGAATCGTATTTGTTTTGGCAGATATGCTCTTCAAACAC
|| || ||| ||||||||||||||||||||||||||||||||| || ||||| || ||||||||||||| |||| ||||||||| |||||||||| ||||||||||||||||||||||||||| |||||||| | || |||| ||| | || || ||| ||||||||||||| ||||||||||||||| |||
cacactttctcatttgattcgcgaggagctggatgagaagaaactctcatgtccagttttgcagtagagatggaa---ctaagagagaaccatcgactataacCCCAAAAGAACCAGATTTCGTAAACAACATAGAGGAAGAATGAAGGGAAAATCCTACCGAGGCAATTGTATTTGTTTTGGTAGATATGCTCTTCAAGCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acgttcagttctgtagtagagatggaatttctaatttagaaccatcaactataacCCAAAAAGAACCAGATTTCGTAAACAACATCGAGGAAGACTAAAAGGAATATCTTCTCGTGGGAATCGTATTTGTTTTGGCAGATATGCTCTTCAAACAC
ttctaat putative branch site (score: 2)
aatttctaatttagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttagtccttttattcgcgaggagctggatgagaagaaactctcacgttcagttctgtagtagagatggaatttctaatttagaaccatcaactataacCCAAAAAGAACCAGATTTCGTAAACAACATCGAGGAAGACTAAAAGGAATATCTTCTCGTGGGAATCGTATTTGTTTTGGCAGATATGCTCTTCAAACAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - -gaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaacca