Sequence
atgc intronic sequence ATGC exonic sequence...cttcaatggagcactgaataattagtatagtagtagttgcagctgaataatttgtgagactgagacatgaatcaatgctgatggtggtggtggtgtgcagTGGTGCAGCTCTGCTACAACCAGCTCACCGGGGGAGTCCCCACGCAGCTGGGGCTCTTGAAGAGGCTCACCGTGCTGGAGCTGCAGTCCAACCACCTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g39600.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g39600.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G100911_T01 (Zea mays), 3'ss of exon 1
--cttcaatggagcactgaataattagtatagta-gtagttgcagctgaataatttgtgagactgagacatgaatcaatgctgatggtggtggtggtgtgcagTGGTGCAGCTCTGCTACAACCAGCTCACCGGGGGAGTCCCCACGCAGCTGGGGCTCTTGAAGAGGCTCACCGTGCTGGAGCTGCAGTCCAACCACCTCAG
|| | | | | | | | | || ||||| | | | || || || | || ||| || || | |||||||||||||||||||||||||||||||||||||| | |||||||||||||||| | | | |||||||||||||||| ||||||||||||| | |||
ctagccagtactactactacttgtccttgcattgcatatttgcatc--acctacctgaatgaatgctgctgatattgatg-tgtccatgaccacgccgtgcagTGGTGCAGCTCTGCTACAACCAGCTCACCGGGAGCATCCCCACGCAGCTGGGCAACCTCACCAGGCTCACCGTGCTGGCCCTGCAGTCCAACCGCTTCAA
upper sequence: LOC_Os01g39600.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G165428_T01 (Zea mays), 3'ss of exon 1
cttcaatggagcactgaataattagtatagtagtagttgcagctgaataatttgtgagactgagacatgaatcaatgctgatggtggtg-----gtggtg-tgcagTGGTGCAGCTCTGCTACAACCAGCTCACCGGGGGAGTCCCCACGCAGCTGGGGCTCTTGAAGAGGCTCACCGTGCTGGAGCTGCAGTCCAACCACCTCAG
| ||| | | || | | ||||| || || || || | || |||||| |||||||| || | ||| | ||||||||||||||||||||||||||||||||| ||| | ||||||| |||||||| | | | |||||||||||||||| ||||||||||||| |||||
----------gtact-actgcttgtccttgct----ttgcatctccatctcctgcctgattctga-atgaat-gctgctgatgttgatatgtccatggcggtgcagTGGTGCAGCTCTGCTACAACCAGCTCACTGGGAGCATCCCCACCCAGCTGGGCAACCTCAGCAGGCTCACCGTGCTGGCCCTGCAGTCCAACCGCCTCAA
upper sequence: LOC_Os01g39600.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G165428_T02 (Zea mays), 3'ss of exon 1
-cttcaatggagcactgaataattagtatagtagtagttgcagctgaataatttgtgagactgagacatgaatcaatgctgatggtggtg-----gtggtg-tgcagTGGTGCAGCTCTGCTACAACCAGCTCACCGGGGGAGTCCCCACGCAGCTGGGGCTCTTGAAGAGGCTCACCGTGCTGGAGCTGCAGTCCAACCACCTCAG
| | | | ||| | | || | | ||||| || || || || | || |||||| |||||||| || | ||| | ||||||||||||||||||||||||||||||||| ||| | ||||||| |||||||| | | | |||||||||||||||| ||||||||||||| |||||
accgctagccggtact-actgcttgtccttgct----ttgcatctccatctcctgcctgattctga-atgaat-gctgctgatgttgatatgtccatggcggtgcagTGGTGCAGCTCTGCTACAACCAGCTCACTGGGAGCATCCCCACCCAGCTGGGCAACCTCAGCAGGCTCACCGTGCTGGCCCTGCAGTCCAACCGCCTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataatttgtgagactgagacatgaatcaatgctgatggtggtggtggtgtgcagTGGTGCAGCTCTGCTACAACCAGCTCACCGGGGGAGTCCCCACGCAGCTGGGGCTCTTGAAGAGGCTCACCGTGCTGGAGCTGCAGTCCAACCACCTCAG
tgctgat putative branch site (score: 3)
aatcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcaatggagcactgaataattagtatagtagtagttgcagctgaataatttgtgagactgagacatgaatcaatgctgatggtggtggtggtgtgcagTGGTGCAGCTCTGCTACAACCAGCTCACCGGGGGAGTCCCCACGCAGCTGGGGCTCTTGAAGAGGCTCACCGTGCTGGAGCTGCAGTCCAACCACCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG