Sequence
atgc intronic sequence ATGC exonic sequencegtaattaagagtttgcaacaatataacttgctttacccccagaaatatgcattttgctaacctcttttactgaaatgtcttagGATCGTACAGCACGAGGAATTTATGACTTATGCGAGTTCACTAAAAGGCTGGATAAGAGCCCCAAAACTGATACTCGTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g01070.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g01070.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G078711_T01 (Zea mays), 3'ss of exon 9
gtaattaagagtttgcaacaatataacttgctttacccccagaaatatgcattttgctaacc--tcttttactgaaatgtcttagGATCGTACAGCACGAGGAATTTATGACTTATGCGAGTTCACTAAAAGGCTGGATAAGAGCCCCAAAACTGATACTCGTCAG
|| ||| | || | | ||| ||| | ||||| | | |||||| | ||| ||||||||||||||||||||| ||| |||||||||| ||||| || || || ||||||||||| ||||| ||||||| ||| |||| |||| ||||
----gtagacatttacctcactgt--cttatttttctcccagtgac-tcaattttgtttcttaatctcatactgaaatgtcttagGATCGGACAACACGAGGAATATATGATTTGTGTGAATTCACTAAAAGATTGGATCAGAGCCCGAAAGCTGAGACTCATCAG
upper sequence: LOC_Os01g01070.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G147587_T01 (Zea mays), 3'ss of exon 9
gtaattaagagtttgcaacaatataacttgctttacccccagaaatatgcattttgctaacctcttttactgaaatgtcttagGATCGTACAGCACGAGGAATTTATGACTTATGCGAGTTCACTAAAAGGCTGGATAAGAGCCCCAAAACTGATACTCGTCAG
||| || ||| || || | | | ||| ||| || | || || |||| ||| | |||||||||||||||||||| ||| |||||||||| ||||| || || || ||||||||||| ||||| ||||||| ||| ||||||||||||||
gtatgtagacatttacatcactgactcattcttctcccagcgactcaattatatttctaatctcat--actgaaatgtcttagGATCGGACAACACGAGGAATATATGATTTGTGTGAATTCACTAAAAGATTGGATCAGAGCCCGAAAGCTGATACTCGTCAG
upper sequence: LOC_Os01g01070.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G432653_T01 (Zea mays), 3'ss of exon 4
gtaattaagagtttgcaacaatataacttgctttacccccagaaatatgcattttgctaacctcttttactgaaatgtcttagGATCGTACAGCACGAGGAATTTATGACTTATGCGAGTTCACTAAAAGGCTGGATAAGAGCCCCAAAACTGATACTCGTCAG
|| ||| || || | | | ||| ||| || | || || |||| ||| | |||||||||||||||||||| ||| |||||||||| ||||| || || || ||||||||||| ||||| ||||||| ||| ||||||||||||||
----gtagacatttacatcactgactcattcttctcccagcgactcaattatatttctaatctcat--actgaaatgtcttagGATCGGACAACACGAGGAATATATGATTTGTGTGAATTCACTAAAAGATTGGATCAGAGCCCGAAAGCTGATACTCGTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctttacccccagaaatatgcattttgctaacctcttttactgaaatgtcttagGATCGTACAGCACGAGGAATTTATGACTTATGCGAGTTCACTAAAAGGCTGGATAAGAGCCCCAAAACTGATACTCGTCAG
tgctaac putative branch site (score: 1)
agaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattaagagtttgcaacaatataacttgctttacccccagaaatatgcattttgctaacctcttttactgaaatgtcttagGATCGTACAGCACGAGGAATTTATGACTTATGCGAGTTCACTAAAAGGCTGGATAAGAGCCCCAAAACTGATACTCGTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA