Sequence
atgc intronic sequence ATGC exonic sequenceCAATGGACCTGAAATACATGATGAGAGAGGGATCGAATGCATGAGGGCTTCTGGAAAGCTTGCTGCACAAGTTTTGAAGTTTGCCGGGACTCTTGTAGAGgtaatgctattattactaaaaattttatattctaacttttgaattgattgaacattattaacattagggaaacttcatcccgttccgtattgaaaaaaca...
Basic information
species | Oryza sativa |
transcript | LOC_Os02g52420.3 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g52420.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G101438_T02 (Zea mays), 5'ss of exon 3
CAATGGACCTGAAATACATGATGAGAGAGGGATCGAATGCATGAGGGCTTCTGGAAAGCTTGCTGCACAAGTTTTGAAGTTTGCCGGGACTCTTGTAGAGgtaatgctattattactaaaaattttatattctaacttttgaattgattgaacattattaacattagggaaacttcatcccgttccgtattgaaaaaaca------
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TAATGGACCTGAAATACATGATGAGAACGGGATCGAGTGCATGAGAGCTTCTGGAAAGCTTGCTGCACAGGTTTTGAAATTTGCTGGGACTCTTGTAAAGgtaatgtcat-gttgctacaaaa-----gcttgaccttttcaatcagtaaactgtcttttccactagataaaccttattcattctacagtttttaaagtagtttac
upper sequence: LOC_Os02g52420.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv07s0031g00820.t01 (Vitis vinifera), 5'ss of exon 3
CAATGGACCTGAAATACATGATGAGAGAGGGATCGAATGCATGAGGGCTTCTGGAAAGCTTGCTGCACAAGTTTTGAAGTTTGCCGGGACTCTTGTAGAGgtaatgctattattactaaaaatt--ttatattctaacttttgaattgattgaacattattaacattagggaaacttcat---cccgttccgtattgaaaaaaca
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GAGTGGACCAGAAGTGCATGATGAGAAGGGGATAGAATGCATGAGGAATTCTGGAAGGCTTGCAGCACAGGTCCTTGAATATGCTGGGACTTTAGTCAAGgtgacatcatagttgtttcatctcaatctcattccctctttcacttcactcccattgaacttttgggaatgatttttcattttccttttcctttttgttc-----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
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAATGGACCTGAAATACATGATGAGAGAGGGATCGAATGCATGAGGGCTTCTGGAAAGCTTGCTGCACAAGTTTTGAAGTTTGCCGGGACTCTTGTAGAGgtaatgctattattactaaaaattttatattctaacttttgaattgattgaacattattaacattagggaaacttcatcccgttccgtattgaaaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG