Sequence
atgc intronic sequence ATGC exonic sequenceGGCGTACGATCGGGCGGCGATCAAGTTCCGCGGCGTGGAGGCCGACATCAATTTCAGCTTGGAGGATTACGAGGATGACCTGAAGCAGgtgagagcgcgatcgattattattacctgaactttcctttcttttcatgagtcgccacggtttcgttagatcatactactattactgtagctgcaagattaacgggatcattgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g55560.3 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g55560.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G174784_T02 (Zea mays), 5'ss of exon 3
GGCGTACGATCGGGCGGCGATCAAGTTCCGCGGCGTGGAGGCCGACATCAATTTCAGCTTGGAGGATTACGAGGATGACCTGAAGCAGgtgagagcgcgatcgattattattacctgaactttcctttcttttcatgagtcgccacggtttcgttagatcatactactattactgtagctgcaagattaacgggatcattgcag
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GGCGTACGATCGGGCGGCGATCAAGTTCCGCGGCGTGGAGGCCGACATCAATTTCAGTCTGGAGGATTACCAGGACGACATGAAGCAGgtga--------tttat-actcctatacggagcatgtagcgagaaagatacatgtaattttttctttccttcgt-ctaccag----------------------------------
upper sequence: LOC_Os04g55560.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G076602_T01 (Zea mays), 5'ss of exon 3
GGCGTACGATCGGGCGGCGATCAAGTTCCGCGGCGTGGAGGCCGACATCAATTTCAGCTTGGAGGATTACGAGGATGACCTGAAGCAGgtgagagcgcgatcgattattat-tacctgaactttcctttcttttcatgagtcgccacggtttcgttagatcatacta--ctat-tactgtagctgcaagattaacgggatcattgcag
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GGCGTACGATCGAGCGGCGATCAAGTTCCGCGGCGTGGAGGCCGACATCAATTTCAGCTTGGAGGATTACCAAGACGACATGAAGCAGgtgat-------ttatttattatacaactgcgctatactaggtagcatatagcaacaatatatatagtaattttttctcgtctatctaatccacgtcttggtctaccagcag--------
upper sequence: LOC_Os04g55560.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G174784_T03 (Zea mays), 5'ss of exon 3
GGCGTACGATCGGGCGGCGATCAAGTTCCGCGGCGTGGAGGCCGACATCAATTTCAGCTTGGAGGATTACGAGGATGACCTGAAGCAGgtgagagcgcgatcgattattattacctgaactttcctttcttttcatgagtcgccacggtttcgttagatcatactactattactgtagctgcaagattaacgggatcattgcag
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GGCGTACGATCGGGCGGCGATCAAGTTCCGCGGCGTGGAGGCCGACATCAATTTCAGTCTGGAGGATTACCAGGACGACATGAAGCAGgtga--------tttat-actcctatacggagcatgtagcgagaaagatacatgtaattttttctttccttcgt-ctaccagcag-------------------------------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|29644662|gb|CB649669.1|CB649669EST: AGGCCGACATCAATTTCAGCTTGGAGGATTACGAGGATGACCTGAAGCAG ATGAGCAACCTGACCAAGGAGGAGTTCGTCCACGTGCTCCGGCGGCAGAGC
genomic: AGGCCGACATCAATTTCAGCTTGGAGGATTACGAGGATGACCTGAAGCAGgtgagagcgc ... atcattgcagATGAGCAACCTGACCAAGGAGGAGTTCGTCCACGTGCTCCGGCGGCAGAGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGCGTACGATCGGGCGGCGATCAAGTTCCGCGGCGTGGAGGCCGACATCAATTTCAGCTTGGAGGATTACGAGGATGACCTGAAGCAGgtgagagcgcgatcgattattattacctgaactttcctttcttttcatgagtcgccacggtttcgttagatcatactactattactgtagctgcaagattaacgggatcattgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC