Sequence
atgc intronic sequence ATGC exonic sequenceGATGGAAATGGGTGGTGGCAGTTGGGACAGAGATAAAGTCCAAAGAGCTCTACGTGCAGCTTATAACAACCCAGAGCGTGCTGTTGAATATCTATATTCTgtatgttctgtttcctcctgtaaatgtttgttattcttttttttctaacgttaatagataatgtttgtttctcccaaacattag
Basic information
species | Oryza sativa |
transcript | LOC_Os02g08300.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g08300.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G143462_T06 (Zea mays), 5'ss of exon 6
GATGGAAATGGGTGGTGGCAGTTGGGACAGAGATAAAGTCCAAAGAGCTCTACGTGCAGCTTATAACAACCCAGAGCGTGCTGTTGAATATCTATATTCTgtatgttctgtttcctcctgtaaatgtttgttattcttttttttctaacgttaatagataatgtt---------------tgtttctcccaaacattag
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AATGGAGATGGGTGGGGGCAGTTGGGACAAAGATAAAGTCCAAAGGGCTCTCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtatt-tttctcattgccccattcttttgcatttttgcacttaatgatggaatccaattttctggtgctaatagattatttatgtcaaacattag
upper sequence: LOC_Os02g08300.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G143462_T05 (Zea mays), 5'ss of exon 6
GATGGAAATGGGTGGTGGCAGTTGGGACAGAGATAAAGTCCAAAGAGCTCTACGTGCAGCTTATAACAACCCAGAGCGTGCTGTTGAATATCTATATTCTgtatgttctgtttcctcctgtaaatgtttgttattcttttttttctaacgttaatagataatgtt---------------tgtttctcccaaacattag----------
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AATGGAGATGGGTGGGGGCAGTTGGGACAAAGATAAAGTCCAAAGGGCTCTCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtatt-tttctcattgccccattcttttgcatttttgcacttaatgatggaatccaattttctggtgctaatagattatttatgtcaaacattagggtattccag
upper sequence: LOC_Os02g08300.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA15G00430.1 (Glycine max), 5'ss of exon 1
GATGGAAATGGGTGGTGGCAGTTGGGACAGAGATAAAGTCCAAAGAGCTCTACGTGCAGCTTATAACAACCCAGAGCGTGCTGTTGAATATCTATATTCTgtatgttctgtttcctc-ctgtaaatgtttgttattc----ttttttttctaacgttaatagat-aatgtttgtttctc--ccaaacattag---
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TATGGACCTGGGTGGTGGCAGTTGGGACAGAGATACAGTTAGTCGTGCTCTTCGAGCAGCTTACAATAACCCAAAGCGTGCTGTAGATTATTTATATTCTgtattccttaagtgctcattgtagaatctaactgcttaaattttctgctgcatcttttgcaatttagcaattatttatgtactttttgtttgcag
upper sequence: LOC_Os02g08300.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA13G44910.2 (Glycine max), 5'ss of exon 6
GATGGAAATGGGTGGTGGCAGTTGGGACAGAGATAAAGTCCAAAGAGCTCTACGTGCAGCTTATAACAACCCAGAGCGTGCTGTTGAATATCTATATTCTgtatgttc----tgtttcctcctgtaaatgtttg-ttattcttttttttctaacgttaatagat-aatgtttgtttctcccaaacattag
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TATGGACATGGGTGGCGGCAGTTGGGACAGAGATACAGTTACTTGTGCTCTTCGAGCAGCTTACAATAACCCAGAGCGTGCTGTAGATTACTTGTATTCTgtatgcctgaagtgctcattgttgaatctaactgcttagattttctgctgtatcttttgcaatttagcaattatttctttttgtttgcag
upper sequence: LOC_Os02g08300.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G00490.1 (Glycine max), 5'ss of exon 6
GATGGAAATGGGTGGTGGCAGTTGGGACAGAGATAAAGTCCAAAGAGCTCTACGTGCAGCTTATAACAACCCAGAGCGTGCTGTTGAATATCTATATTCTgtatgttctgtttcctcctgt-----aaatgtttgttattcttttttttctaacgttaatagataatgtttgtt---tctcccaaacattag-------------
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TATGGACATGGGTGGTGGCAATTGGGACAGAGACACAGTTAGTCGTGCTCTTCGGGCAGCTTATAATAACCCAGAGCGTGCTATAGATTATTTGTATTCTgtatgtcttaactgcttgtattttttgaatgcttaaaatt-ttctgttgtaaatgtttggatttaacaattcttcaattttttgtgcttttttgctttttggcag
upper sequence: LOC_Os02g08300.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G16190.1 (Arabidopsis thaliana), 5'ss of exon 6
GATGGAAATGGGTGGTGGCAGTTGGGACAGAGATAAAGTCCAAAGAGCTCTACGTGCAGCTTATAACAACCCAGAGCGTGCTGTTGAATATCTATATTCTgtatgttctgtttcctcctgtaaatgtttgttattcttttttttctaacgttaatagataatgtttgtttctcccaaacattag
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AATGGAAATGGGAGGAGGCAGTTGGGACAAAGAAACGGTTACTCGTGCACTTCGTGCAGCATATAACAACCCTGAGAGAGCAGTGGATTATCTATATTCTgtatgccccttctc----tgtaacagt--gttctgtgaatatttgaagggattgaaactgctgat-gtctattttaattttcagMapped 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|58680913|gb|CK069600.1|CK069600EST: TACGTGCAGCTTATAACAACCCAGAGCGTGCTGTTGAATATCTATATTCT GGCATTCCAATTACAGCGGAGGTTGCTGTTCC
genomic: TACGTGCAGCTTATAACAACCCAGAGCGTGCTGTTGAATATCTATATTCTgtatgttctg ... caaacattagGGCATTCCAATTACAGCGGAGGTTGCTGTTCC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATGGAAATGGGTGGTGGCAGTTGGGACAGAGATAAAGTCCAAAGAGCTCTACGTGCAGCTTATAACAACCCAGAGCGTGCTGTTGAATATCTATATTCTgtatgttctgtttcctcctgtaaatgtttgttattcttttttttctaacgttaatagataatgtttgtttctcccaaacattag
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT