Sequence
atgc intronic sequence ATGC exonic sequence...tcatctgatatatgtctctgcttgtttctcagacttaccatactctagggatgtataaaactcaagtgtcaaagactgatttgttcttattgacagccagGCATAACAACTGATGAGATTGATAAAGCGGTGCACCAAATGATAGTAGATAATGGAGCATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g52420.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g52420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G101438_T04 (Zea mays), 3'ss of exon 3
--tcatctgatatatgtctctgcttgtttctcagacttaccatactctagggatgtataaaactcaagtgtcaaagactgatttgttcttattgacagccagGCATAACAACTGATGAGATTGATAAAGCGGTGCACCAAATGATAGTAGATAATGGAGCATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGT
|||||||| || | |||| |||| |||| || || ||| | | | || || || ||| |||||| | ||||||||||||||||||||| |||||||| ||||||||||| ||||||||||||||| | |||||||||||||| ||||| || ||||||||||| || | |||||||||||
ttccatctgatgtacgactctttgctattcttcagcttagtatttacttggg--gatctgagtttaaatgccagagaatgattttattttattgacagccagGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATTGATAATGGAGCATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGAGTGT
upper sequence: LOC_Os02g52420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G101438_T02 (Zea mays), 3'ss of exon 3
------tcatctgatatatgtctctgcttgtttctcagacttaccatactctagggatgtataaaactcaagtgtcaaagactgatttgttcttattgacagccagGCATAACAACTGATGAGATTGATAAAGCGGTGCACCAAATGATAGTAGATAATGGAGCATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGT
|||||||| || | |||| |||| |||| || || ||| | | | || || || ||| |||||| | ||||||||||||||||||||| |||||||| ||||||||||| ||||||||||||||| | |||||||||||||| ||||| || ||||||||||| || | |||||||
ttctttccatctgatgtacgactctttgctattcttcagcttagtatttacttggg--gatctgagtttaaatgccagagaatgattttattttattgacagCCAGGCATAACGACTGATGAAATTGATAAAGCAGTGCACCAAATGATAATTGATAATGGAGCATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGA----
upper sequence: LOC_Os02g52420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G39200.1 (Glycine max), 3'ss of exon 3
tcatctgatat--atgtctctgcttgtttct-cagacttaccatactctagggatgtataaaactcaagtgtcaaagactgatttg-ttcttattgacagccagGCATAACAACTGATGAGATTGATAAAGCGGTGCACCAAATGATAGTAGATAATGGAGCATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGT
| || | | || | || | || | | || || | | | |||| | | | | | | ||| | | ||||||||||||||||||||| ||||| ||||| |||| || |||||||||||| | |||||||| |||||||| || || || || ||| | ||||||| ||||
ttatgaagtgttaataattttgtataattatactgattttatgtttttattttaaaagaaaaagttgtttttttatgttagttttaacttctgttgacagCCAGGCATAACAACAGATGAAATTGACCAAGCAGTTCACCAAATGATAATTGATAATGGTGCATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGA----Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29657569|gb|CB653844.1|CB653844EST: CTGGAAAGCTTGCTGCACAAGTTTTGAAGTTTGCCGGGACTCTTGTAGAG GCATAACAACTGATGAGATTGATAAAGCGGTGCACCAAATGATAGTAGATA
genomic: CTGGAAAGCTTGCTGCACAAGTTTTGAAGTTTGCCGGGACTCTTGTAGAGgtaatgctat ... tgacagccagGCATAACAACTGATGAGATTGATAAAGCGGTGCACCAAATGATAGTAGATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagggatgtataaaactcaagtgtcaaagactgatttgttcttattgacagccagGCATAACAACTGATGAGATTGATAAAGCGGTGCACCAAATGATAGTAGATAATGGAGCATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGT
tattgac putative branch site (score: 2)
ttcttatt CT-rich tract
atgtataaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatctgatatatgtctctgcttgtttctcagacttaccatactctagggatgtataaaactcaagtgtcaaagactgatttgttcttattgacagccagGCATAACAACTGATGAGATTGATAAAGCGGTGCACCAAATGATAGTAGATAATGGAGCATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
-catctga
- - - - - - - - -ctgcttg
- - - - - - - - - - - - - - - - - - - catactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaagac