Sequence
atgc intronic sequence ATGC exonic sequencegtaacatttacttgttgctgtgttttgagaagtgcaagagcacaacctcgctataggagagggaaaaaagtttgtccataaaagttagtatttataattcgtgctaactaatgtgaaaacaactcagGTGTGCATATTTGCATATGGCCAAACTGGCTCGGGTAAAACATACACAATGATGGGAAATCCAGAATTGCATGACCAGAAAGGATTAATTCCGAGATCAC
Basic information
species | Oryza sativa |
transcript | LOC_Os07g01490.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g01490.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G436981_T02 (Zea mays), 3'ss of exon 10
gtaacatttacttgttgctgtgttttgagaagtgcaagagcacaacctcgctataggagagggaaaaaagtttgtccat-----aaaagttagtatttataattcgtgctaactaatgtgaaaacaactcagGTGTGCATATTTGCATATGGCCAAACTGGCTCGGGTAAAACATACACAATGATGGGAAATCCAGAATTGCATGACCAGAAAGGATTAATTCCGAGATCAC
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-----gtata-tcatt--tgtatgactataactgagattaccttctctaactctagtaactatgatttttttggttcgttttccaatatctagttttcttagaatgcaactaaaaaccagtaaaccatttagGTCTGCATATTTGCCTATGGGCAAACTGGTTCTGGTAAAACATATACAATGATGGGCAACCCTGAGTTAGAAGATCAAAAAGGAATGATACCACGATCTC
upper sequence: LOC_Os07g01490.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ27367 (Selaginella moellendorffii), 3'ss of exon 9
gtaacatttacttgttgctgtgttttgagaagtgcaagagcacaacctcgctataggagagggaaaaaagtttgtccataaaagttagtatttataattcgtgctaactaat-gtgaaaacaactcagGTGTGCATATTTGCATATGGCCAAACTGGCTCGGGTAAAACATACACAATGATGGGAAATCCAGAATTGCATG-ACCAGAAAGGATTAATTCCGAGATCAC
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-----------------------------------------------------------------------------gtaacacct--tttcttttgttggcattctctgtttaccttgtccttgtagGTTTGCATATTTGCGTATGGCCAAACTGGATCGGGCAAGACACACACTATGATTGGACAGCCAGA-TGACATGGACCAGAAGGGTGTGATTCCCAGGTCCT
upper sequence: LOC_Os07g01490.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ33133 (Selaginella moellendorffii), 3'ss of exon 10
gtaacatttacttgttgctgtgttttgagaagtgcaagagcacaacctcgctataggagagggaaaaaagtttgtccataaaagttagtatttataattcgtgctaactaat-gtgaaaacaactcagGTGTGCATATTTGCATATGGCCAAACTGGCTCGGGTAAAACATACACAATGATGGGAAATCCAGAATTGCATG-ACCAGAAAGGATTAATTCCGAGATCAC
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-----------------------------------------------------------------------------gtaacacct--tttcttttgttggcattctctgtttaccttgtccttgtagGTTTGCATATTTGCGTATGGCCAAACTGGATCGGGCAAGACACACACTATGATTGGACAGCCAGA-TGACATGGACCAGAAGGGTGTGATTCCCAGGTCTTMapped 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|157651703|gb|EX451337.1|EX451337EST: TGTTCATTGAGATTTCCCAACTCGTCCAAAGCGCCCTTGATGGCTACAAG GTGTGCATATTTGCATATGGCCAAACTGGCTCGGGTAAAACATACACAATG
genomic: TGTTCATTGAGATTTCCCAACTCATCCAAAGCGCCCTTGATGGCTACAAGgtaacattta ... aacaactcagGTGTGCATATTTGCATATGGCCAAACTGGCTCGGGTAAAACATACACAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtccataaaagttagtatttataattcgtgctaactaatgtgaaaacaactcagGTGTGCATATTTGCATATGGCCAAACTGGCTCGGGTAAAACATACACAATGATGGGAAATCCAGAATTGCATGACCAGAAAGGATTAATTCCGAGATCAC
ataaaagttagtattt TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacatttacttgttgctgtgttttgagaagtgcaagagcacaacctcgctataggagagggaaaaaagtttgtccataaaagttagtatttataattcgtgctaactaatgtgaaaacaactcagGTGTGCATATTTGCATATGGCCAAACTGGCTCGGGTAAAACATACACAATGATGGGAAATCCAGAATTGCATGACCAGAAAGGATTAATTCCGAGATCAC
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