Sequence
atgc intronic sequence ATGC exonic sequence...gccctcttttcttagcattcttccttcaaggaatgcaaaagtgagcactaaacaactgtaatactaattaagcatcatatattattgcttgcaaatgcagGTGCTACTACAGGTGCACGTACCATCAGGACCATGGCTGTCCAGCGAGCAAGCACGTGGAGCAGCACAACTCGGAGGACCCGCCTTTGTTCCGGGTGATC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g60490.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g60490.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G029292_T02 (Zea mays), 3'ss of exon 2
gccctcttttcttagcattcttccttcaaggaatgcaaaagtg-agca---ctaaacaactgtaatactaattaagcatcatatattattgcttgcaa--atgcagGTGCTACTACAGGTGCACGTACCATCAGGACCATGGCTGTCCAGCGAGCAAGCACGTGGAGCAGCACAACTCGGAGGACCCGCCTTTGTTCCGGGTGATC
|| | | | || || | | | || |||| | ||| | |||| | | || | | || | ||| | | | ||||||||||||||| ||||| || ||||| ||||| |||||||| ||||| | ||| || |||||||| |||| ||| |||| ||||| |||||||||| |||
-----tattggaaaactgagcttaaacagaaaaagttagactgtagcaagtttggccaaacaaactactcttgatgc-taaactactcttgatatctaccatgcagGTGCTACTATAGGTGTACATACCACCAGGATCATGGCTGCCCAGCAACCAAACATGTGGAGCAAAACAATTCGCAGGATCCGCCACTGTTCCGGGTAATC
upper sequence: LOC_Os01g60490.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G382350_T01 (Zea mays), 3'ss of exon 2
gccctcttttcttagcattcttccttcaaggaatgcaaaag---tgagcactaaacaactgtaatactaattaagcatcatatattattgcttgcaaatgcagGTGCTACTACAGGTGCACGTACCATCAGGACCATGGCTGTCCAGCGAGCAAGCACGTGGAGCAGCACAACTCGGAGGACCCGCCTTTGTTCCGGGTGATC
| ||||| |||| | | | | | || | | | ||| | | || || | | | | || || | || ||||||||||||||| |||||||| ||||| ||||| |||||||| ||||| | |||||| |||||||| ||| || |||||||||| ||||||||||| | |
--cggcttttacaggcatgcatgtatgcatgttggcgacctcttttttccctaggtcatggaaaagtgaactctaaactac-tcttgatgtctacacatgcagGTGCTACTATAGGTGCACATACCACCAGGATCATGGCTGCCCAGCAACCAAGCATGTGGAGCAAACCAATTCCCAGGACCCGCCATTGTTCCGGGTAACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactaaacaactgtaatactaattaagcatcatatattattgcttgcaaatgcagGTGCTACTACAGGTGCACGTACCATCAGGACCATGGCTGTCCAGCGAGCAAGCACGTGGAGCAGCACAACTCGGAGGACCCGCCTTTGTTCCGGGTGATC
tactaat putative branch site (score: 1)
taatactaattaagca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccctcttttcttagcattcttccttcaaggaatgcaaaagtgagcactaaacaactgtaatactaattaagcatcatatattattgcttgcaaatgcagGTGCTACTACAGGTGCACGTACCATCAGGACCATGGCTGTCCAGCGAGCAAGCACGTGGAGCAGCACAACTCGGAGGACCCGCCTTTGTTCCGGGTGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - -agcattc
- - - - - - - - - - -tccttca
- - - - - - - - - - - - - - - gaatgca
- - - - - - - - - - - - - - - - - - - - - - - - - aacaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tattgct