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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCACGAACACAGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATAATTTCAAGgtatatccatctatccttttatccatttgctctgcaataatatactagcgtctgaaatttagttcaatttatgtgaggttacttacatgacttgtattatctggttgtatcag

Basic information

species Oryza sativa
transcript LOC_Os04g04020.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g04020.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G143725_T01 (Zea mays), 5'ss of exon 5
AAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCACGAACACAGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATAATTTCAAGgtatatcc---atctatccttttatccatttgctctgcaataatatactagcgtctgaaatttagtt-caatttatgtgaggt------------tacttacatgacttgtattatctggttgtatcag
||||||||| ||||||||||| ||||| || ||||| ||||| ||||||||||||||||||||||| ||||| || || ||||| |||||||| ||||||| ||   |   |||| ||   |  ||  ||| |    |||   ||  ||   || |   |||   |  |||||| ||   | |            |||| | |  || |||||  | |  |||||||||
AAAGACCATAAAATCATGCCTCGATGAACTTCCAGGCTTTCCGCGAACACAGATTGGATTCTTAACATTTGACAGTACCTTGCATTTTCATAACTTCAAGgcatgctctgtatctctcacatagtcatttttcaactcaaacttaaccttttgttttgcattacatggcaatttttgaatgttgcattcaatatgtactaaaagaacctgtatggttttcttgtatcag

upper sequence: LOC_Os04g04020.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G081745_T01 (Zea mays), 5'ss of exon 4
AAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCACGAACACAGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATAATTTCAAGgtatatccatctatccttttatccatttgctctgcaataatatactagcgtctgaaatttagttcaatttatgtgaggttacttacatgacttgtattatctggttgtatcag
||||||||||||||||||||||||||| || ||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||| |||||||| ||||||| || | | |  |||  |     ||| |   ||   ||||   |  ||  |||    ||  || |  |     |      |   |||  |  ||    |||  |         
AAAGACCATCAAATCATGCCTTGATGAACTTCCAGGCTTTCCACGAACACAGATTGGATTCTTAACCTTTGACAGCACCTTGCATTTTCATAACTTCAAGgcatgttc-tacatctctc---acatctctactaatataaagcataagtttcttcctttgcgtcc--tccccctcccacaatcgacaaaaaatgctgcatccagga-------
















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|29633800|gb|CB638809.1|CB638809
EST:     AGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATAATTTCAAG                         TCGTCTTTGTCACATTCCTCAAATGATGGTGGTCGCTGATTTGGATGATGT
genomic: AGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATAATTTCAAGgtatatccat ... gttgtatcagTCGTCTTTGTCACA-ACCTCAAATGATGGTGGTCGCTGATTTGGATGATGT
EST: gi|29624740|gb|CB629751.1|CB629751
EST:     CATAATTTCAAG                         TCGTCTTTGTCACAACCTCAAATGATGGTGGTCGCTGATTTGGATGATGTT
genomic: CATAATTTCAAGgtatatccat ... gttgtatcagTCGTCTTTGTCACAACCTCAAATGATGGTGGTCGCTGATTTGGATGATGTT
EST: gi|88588495|gb|CI706315.1|CI706315
EST:     AGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATAATTTCAAG                         TCGTCTTTGTCACA-CCTCAAATGATGGTGG
genomic: AGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATAATTTCAAGgtatatccat ... gttgtatcagTCGTCTTTGTCACAACCTCAAATGATGGTGG
EST: gi|29633801|gb|CB638810.1|CB638810
EST:     AGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATAATTTCAAG                         TCGTCTTTGTCACAACCTCAAATGATGGTGGTCGCTGATTTGGATGATGTT
genomic: AGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATAATTTCAAGgtatatccat ... gttgtatcagTCGTCTTTGTCACAACCTCAAATGATGGTGGTCGCTGATTTGGATGATGTT
EST: gi|426130|gb|D21986.1|D21986
EST:     AGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATAATTTCAAG                         TCGTCTTTGTCACAACCTCAAATGATGGTGGTCGNTGATTTGGATGATGTT
genomic: AGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATAATTTCAAGgtatatccat ... gttgtatcagTCGTCTTTGTCACAACCTCAAATGATGGTGGTCGCTGATTTGGATGATGTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 71 (upstream exon), 75 (downstream exon)
Score: 14

AAAGACCATCAAATCATGCCTTGATGACCTCCCAGGGTTTCCACGAACACAGATTGGATTCTTAACTTTTGATAGCACATTGCACTTTCATAATTTCAAGgtatatccat ... gttgtatcagTCGTCTTTGTCACAACCTCAAATGATGGTGGTCGCTGATTTGGATGATGTTTTCCTGCCGTTGCCTGATGACCTCTTGGTTAATTTGGTTGACTCTAGAC




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