Sequence
atgc intronic sequence ATGC exonic sequence...caaagtcaaaacgatttataatctaaaaacgcagggtgtagttctcaatcaactaatctcgattatagtttgctaattacgatgtgtttgtttggttcagGTGACCAGAGCCCGGAGAGGGTGGTGCTGGATTGGCCGGCGAGGATGAGGATCGCCGTCGGCGTGGTGCGCGGCTTGTCGTACCTCCACGAGAAGCTGGG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g40550.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g40550.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G122873_T01 (Zea mays), 3'ss of exon 1
caaagtcaaaacgatttataatctaaaaacgcagggtgtagttctcaatcaac-taatctcgattatagtttgctaattacgatgtgtttgtttggtt-cagGTGACCAGAGCCCGGAGAGGGTGGTGCTGGATTGGCCGGCGAGGATGAGGATCGCCGTCGGCGTGGTGCGCGGCTTGTCGTACCTCCACGAGAAGCTGGG
| ||| || | |||| | || | | || ||| ||||| || | | | | |||| | || | | |||| |||||||| ||| | ||| || | ||||| |||| || || ||||| ||||||| ||||||||||||||| || ||| ||||||||||| ||| ||
--gtatggcaaccatct-ccatctga-----ttggttaactagcacagctaacctaatcacgtgacgtgactaatcacctcgatctaattaataactggcagGCGACCAGAGTCCGAACAGGCTGATCCTGGACTGGCAGGGTCGGCTGAGGGTCGCCGTGGGCGTGGTGCGCGGCCTGGCGTTCCTCCACGAGAGGCTCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatcaactaatctcgattatagtttgctaattacgatgtgtttgtttggttcagGTGACCAGAGCCCGGAGAGGGTGGTGCTGGATTGGCCGGCGAGGATGAGGATCGCCGTCGGCGTGGTGCGCGGCTTGTCGTACCTCCACGAGAAGCTGGG
tgctaat putative branch site (score: 2)
tttgttt putative PPT
attatagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaagtcaaaacgatttataatctaaaaacgcagggtgtagttctcaatcaactaatctcgattatagtttgctaattacgatgtgtttgtttggttcagGTGACCAGAGCCCGGAGAGGGTGGTGCTGGATTGGCCGGCGAGGATGAGGATCGCCGTCGGCGTGGTGCGCGGCTTGTCGTACCTCCACGAGAAGCTGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG