Sequence
atgc intronic sequence ATGC exonic sequence...taagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagGGTGATAGTAAGCTGTCCTCAAAGGCTGGTGATGGTTCAGTAAAGAAGGATACAATTGGTCCGCACAGTGGCGCTAGTAGCTCAAGTGCGCAAGGG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g61810.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g61810.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G303465_T02 (Zea mays), 3'ss of exon 3
-taagatctatatttgtgccttagtaaaag-----atctatt-tttgtgcatcaagattcaagatgta-ttgagttctaaccataccactattcctt---attcttggtagGGTGATAGTAAGCTGTCCTCAAAGGCTGGTGATGGTTCAGTAAAGAAGGATACAATTGGTCCGCACAGTGGCGCTAGTAGCTCAAGTGCGCAAGGG
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ctaatgtg-gtagctgtgaacaagttaatactgtcatgtactgtttgcacagccaggcccaggatgcaactgaatactgatcacaattttttttttggaaaATTTTCGTAGGGTGATAGCAAGCTGTCTACAAAGGCTGGCGAGGGCTCTGTAAAGAAGGATGCAATTAGTCCCCATGGTGGCACCAGTAGCTCAAGTAAT------
upper sequence: LOC_Os01g61810.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G303465_T04 (Zea mays), 3'ss of exon 3
taagatctatatttgtgccttagtaaaag-atctatt-tttgtgcatcaagattcaagatgta-ttgagttctaaccataccactattcctt---attcttggtagGGTGATAGTAAGCTGTCCTCAAAGGCTGGTGATGGTTCAGTAAAGAAGGATACAATTGGTCCGCACAGTGGCGCTAGTAGCTCAAGTGCGCAAGGG
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----agctgtgaacaag--ttaatactgtcatgtactgtttgcacagccaggcccaggatgcaactgaatactgatcacaattttttttttggaaaattttcgtagGGTGATAGCAAGCTGTCTACAAAGGCTGGCGAGGGCTCTGTAAAGAAGGATGCAATTAGTCCCCATGGTGGCACCAGTAGCTCAAGTAATCAG---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|157650082|gb|EX449716.1|EX449716EST: GTACAGAGAGATGGAG
genomic: GTACAGAGAGATGGAG
EST:
gi|218487228|gb|FG968027.1|FG968027EST: CACAAGTACAGAGAGATGGAG
genomic: CACAAGTACAGAGAGATGGAG
EST:
gi|25797854|gb|CA753815.1|CA753815EST: CACAAGTACAGAGAGATGGAG
genomic: CACAAGTACAGAGAGATGGAG
EST:
gi|1631561|gb|C19290.1|C19290EST: CACAAGTACAGAGAGATGGAG
genomic: CACAAGTACAGAGAGATGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caagattcaagatgtattgagttctaaccataccactattccttattcttggtagGGTGATAGTAAGCTGTCCTCAAAGGCTGGTGATGGTTCAGTAAAGAAGGATACAATTGGTCCGCACAGTGGCGCTAGTAGCTCAAGTGCGCAAGGG
ttctaac putative branch site (score: 1)
ctattccttattctt putative PPT
ttattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taagatctatatttgtgccttagtaaaagatctatttttgtgcatcaagattcaagatgtattgagttctaaccataccactattccttattcttggtagGGTGATAGTAAGCTGTCCTCAAAGGCTGGTGATGGTTCAGTAAAGAAGGATACAATTGGTCCGCACAGTGGCGCTAGTAGCTCAAGTGCGCAAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA