Sequence
atgc intronic sequence ATGC exonic sequenceAGACATGTCAACTAACTCAAGGGATCTCATCGAGCGAGAATTGTCTGCGTTTGGTCAGAGCTTGGATAACAGCTTATGCAGGTTGCCAGCAACTCCTCAGgttggtaacattacagtgttaactgtcttagcgagcaggctagcagaatgaaggctataagagccatcatgtgtttctgatctgctgactccttcaatctcttatgtcactgctgtggtttctttttcacag
Basic information
species | Oryza sativa |
transcript | LOC_Os09g21780.2 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g21780.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G116196_T01 (Zea mays), 5'ss of exon 6
AGACATGTCAACTAACTCAAGGGATCTCATCGAGCGAGAATTGTCTGCGTTTGGTCAGAGCTTGGATAACAGCTTATGCAGGTTGCCAGCAACTCCTCAGgttggtaacattacagtgttaactgtcttagcgagcag-gctagcagaatgaaggctataagagccatcatgtgtttctgatctgctgactccttcaatctcttatgtcactgctgtggtttctttttcacag
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AGACATGTCTACGAACTCAAGGGACCTCATAGAGCGAGAGTTAGCTGCATTTAGCCAGAGCTTGGATAATAGCTTGTGCAGGTTGCCAGCAACCCCTCAGgttagtagtgttatatgcttaaatcgattacttccaaataatatctgtctgctatgttcccataccagtactcgtctat-atctgct--ttacctgaatgaac------------------------------
upper sequence: LOC_Os09g21780.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G055917_T02 (Zea mays), 5'ss of exon 6
AGACATGTCAACTAACTCAAGGGATCTCATCGAGCGAGAATTGTCTGCGTTTGGTCAGAGCTTGGATAACAGCTTATGCAGGTTGCCAGCAACTCCTCAGgttggtaacattacagtgttaactgtcttag--cgagcaggctagcagaatgaaggctataagagccatcatgtgtttctgatctgctgactccttcaatctcttatgtcactgctgtggtttctttttcacag
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AGACATGTCTACGAACTCAAGGGACCTCATAGAGCGAGAATTAGCTGCATTTAGCCAGAGCTTGGATAATAGCTTGTGCAGGTTGCCAGCAACCCCGCAGgttagtagtgttatatgtttaaattgattagttccaaaataatatctgtctgctatgttcctatatcagtatttgtttgt-atccgct--tcacctgaatgaa-------------------------------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|66917271|gb|CX104119.1|CX104119EST: TTGGTCAGAGCTTGGATAACAGCTTATGCAGGTTGCCAGCAACTCCTCAG GCTCTTTTGGAGGCTNTGGGCTCCAATGGTGCTACAGGATCAGAAGCAGTT
genomic: TTGGTCAGAGCTTGGATAACAGCTTATGCAGGTTGCCAGCAACTCCTCAGgttggtaaca ... tttttcacagGCTCTTTTGGAGGCTTTGGGCTCCAATGGTGCTACAGGATCAGAAGCAGTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGACATGTCAACTAACTCAAGGGATCTCATCGAGCGAGAATTGTCTGCGTTTGGTCAGAGCTTGGATAACAGCTTATGCAGGTTGCCAGCAACTCCTCAGgttggtaacattacagtgttaactgtcttagcgagcaggctagcagaatgaaggctataagagccatcatgtgtttctgatctgctgactccttcaatctcttatgtcactgctgtggtttctttttcacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC