Sequence
atgc intronic sequence ATGC exonic sequencegtcagtcccctctttctctctctcgccggcgccgccgtgaaatggaaggaaaagctcaccggagctatggttttgttgcaacagGGGGTACTACCGGTGCAGTAGCTCGAAGGGGTGCCCGGCGAGGAAGCAGGTGGAGAGGAGCCGCTCCGACCCCAACACCTTCATCCTCACCTACACCGGC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g16540.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g16540.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G038158_T01 (Zea mays), 3'ss of exon 2
----------------gtcagtcccctctttctct------ctctcgccggcgccgc---cgtgaaatggaaggaa------aagctcaccgga-gctatggttttgttgcaacagGGGGTACTACCGGTGCAGTAGCTCGAAGGGGTGCCCGGCGAGGAAGCAGGTGGAGAGGAGCCGCTCCGACCCCAACACCTTCATCCTCACCTACACCGGC
||||||| | | ||| ||||||||||| ||| || | ||| ||| | ||||||| ||| | || | |||||||| |||||||| ||||| ||||| ||||||||| ||||| |||||||||||||| | |||||| | ||||||||||| ||||||||||||| ||||||
gtcggtcagctagaacaacagtcccttgcctatctgtcggcttctcgccggcgtcgcgttcgcgtctcggagcgaattaaccgatctcaccgcctgctgctatgttccttgaacagGGGATACTACCGATGCAGCAGCTCCAAGGGGTGCGCGGCGCGGAAGCAGGTGGAGCGCAGCCGCGCGGACCCCAACACTTTCATCCTCACCTTCACCGGG
upper sequence: LOC_Os02g16540.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G048450_T01 (Zea mays), 3'ss of exon 2
-------------gtcagtcccctctttctctctctcgccggcgccgccgtgaaatggaaggaaa---agctcaccgga-gctatggttttgttgcaacagGGGGTACTACCGGTGCAGTAGCTCGAAGGGGTGCCCGGCGAGGAAGCAGGTGGAGAGGAGCCGCTCCGACCCCAACACCTTCATCCTCACCTACACCGGC
|| |||| | |||||||| | |||| ||| | | | ||| | ||||||| ||| || | |||||||| |||||||||||||| ||||| |||||||| ||||| |||||||||| ||| | |||||| | |||||||||||||||||||||||||||||||||
gtcggtcagccagaacaatcccttgtttctctcacagcttcttgccggcgtcgcgtcggggcaaaccgatctcaccgcctgctgctcaatttcttgaacagGGGATACTACCGGTGCAGCAGCTCCAAGGGGTGTGCGGCGCGGAAGCAGGTCGAGCGCAGCCGCGCGGACCCCAACACCTTCATCCTCACCTACACCGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgccgccgtgaaatggaaggaaaagctcaccggagctatggttttgttgcaacagGGGGTACTACCGGTGCAGTAGCTCGAAGGGGTGCCCGGCGAGGAAGCAGGTGGAGAGGAGCCGCTCCGACCCCAACACCTTCATCCTCACCTACACCGGC
agctcac putative branch site (score: 3)
ttttgtt putative PPT
ttttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtcccctctttctctctctcgccggcgccgccgtgaaatggaaggaaaagctcaccggagctatggttttgttgcaacagGGGGTACTACCGGTGCAGTAGCTCGAAGGGGTGCCCGGCGAGGAAGCAGGTGGAGAGGAGCCGCTCCGACCCCAACACCTTCATCCTCACCTACACCGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG