Sequence
atgc intronic sequence ATGC exonic sequenceGCAGCTCGCAATATACACTGGTCCAACAGgtatgcatttttatttttatgatttataacctattacaaaatggagaaccagtgaacaataacagacattttcttttaataccgattgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g55940.2 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G040017_T02 (Zea mays), 5'ss of exon 4
GCAGCTCGCAATATACACTGGTCCAACAGgtatgcatttttatttttatgatttataacctattacaaa--atggagaaccagtgaac---aataacagacattttcttttaataccgattgcag
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GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctctttctctttatggctaatagccaatttgaaataatactagatgagggtcctcgaatggcgactgatttcaactttcctgaactgcag
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G143356_T02 (Zea mays), 5'ss of exon 5
GCAGCTCGCAATATACACTGGTCCAACAGgtatgcatttttatttttatgatttataacctattacaaaatggagaaccagtgaacaataacagacattttcttttaataccgattgcag
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GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctctttctctgtatggctaatagtcaacttgaaataagactataagagagtcct--caaatggtgacttactg----aactgcagMapped 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|88763180|gb|CI772736.1|CI772736EST: GCAGCTCGCAATATACACTGGTCCAACAG TTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAG
genomic: GCAGCTCGCAATATACACTGGTCCAACAGgtatgcattt ... ccgattgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCAGCTCGCAATATACACTGGTCCAACAGgtatgcatttttatttttatgatttataacctattacaaaatggagaaccagtgaacaataacagacattttcttttaataccgattgcag
CAGCTC