Sequence
atgc intronic sequence ATGC exonic sequence...gttacaatctctttttttttgtacttgatctaataatatatctagctattatattatctcgaaatatgcttaatacttaattgctatttgaacatttcagTCCTTCGAGTTTGGGATGTGCTTCTGTTTGATGGAAATCGCGTGATGCTCTTTCGAACAGCTCTTGCCCTAATGGAGTTGTATG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g61860.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g61860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G096470_T01 (Zea mays), 3'ss of exon 9
gttacaatctctttttttttgtacttgatctaataatatatctagctattatattatctcgaaatatgcttaatacttaattgctattt--gaacatttcagTCCTTCGAGTTTGGGATGTGCTTCTGTTTGATGGAAATCGCGTGATGCTCTTTCGAACAGCTCTTGCCCTAATGGAGTTGTATG
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agtatgcttggactaatattctgtttc-ttgagtagactata-agctattatcttctctagaaacattcttagcattttactgctatttttaaacatttcagTGCTTCGTGTGTGGGATGTTCTTCTCTTTGAGGGAAACCGTGTGATGCTGTTCCGGACAGCTCTTGCACTGATGGAGTTGTATG
upper sequence: LOC_Os01g61860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 9
-------------------------------gttacaatctctttttttttgtacttgatctaataatatatctagctattatattatctcgaaatatgcttaatacttaattgctatt-tgaacatttcagTCCTTCGAGTTTGGGATGTGCTTCTGTTTGATGGAAATCGCGTGATGCTCTTTCGAACAGCTCTTGCCCTAATGGAGTTGTATG
|| | | || || | ||| | | || | | | | | ||| | | | | | | |||| ||| | | |||||| |||||||| |||||||||||||| ||||| ||||| || || ||||||||| |||| || |||| |||||||| | ||||
gtcaggttttatgttctatctattgagtagcgtagcttagtattgcttcacaaagttgccaatgtcaaatgagcatttgt-acactattgttcgagcttccttctgatctattgtaattatttggacttcagTTCTTCGAGTGTGGGATGTGCTTCTTTTTGAAGGAAACCGAGTCATGCTCTTTAGAACTGCAGTTGCTTTAATGGAGCTATATG
upper sequence: LOC_Os01g61860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 9
-------------------------------gttacaatctctttttttttgtacttgatctaataatatatctagctatta--tattatctcgaaatatgcttaatacttaattgctatttgaacatttcagTCCTTCGAGTTTGGGATGTGCTTCTGTTTGATGGAAATCGCGTGATGCTCTTTCGAACAGCTCTTGCCCTAATGGAGTTGTATG
|| | |||| || | ||| | | || | | | |||| | | | | || | | | |||||| || |||||| |||||||| |||||||||||||| ||||| ||||| || || ||||||||| |||| || |||| |||||||| | ||||
gtcaggttttatgttctatctatttagtagtgtagcctagtcttacttcacaaagttgccaatgtgaaatgagcatttgtacgctattgtttgagcttccttctgatccattgtaattatttggac--ttcagTTCTTCGAGTGTGGGATGTGCTTCTTTTTGAAGGAAACCGAGTCATGCTCTTTAGAACTGCAGTTGCTTTAATGGAGCTATATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctattatattatctcgaaatatgcttaatacttaattgctatttgaacatttcagTCCTTCGAGTTTGGGATGTGCTTCTGTTTGATGGAAATCGCGTGATGCTCTTTCGAACAGCTCTTGCCCTAATGGAGTTGTATG
acttaat putative branch site (score: 4)
aaatatgcttaatact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttacaatctctttttttttgtacttgatctaataatatatctagctattatattatctcgaaatatgcttaatacttaattgctatttgaacatttcagTCCTTCGAGTTTGGGATGTGCTTCTGTTTGATGGAAATCGCGTGATGCTCTTTCGAACAGCTCTTGCCCTAATGGAGTTGTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC