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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggtcatattctcatagcagcagttttttttaataaatggcgttctgtaacctatcctcttggtttctttttgcag

Basic information

species Zea mays
transcript GRMZM2G164265_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164265_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 9
CATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggtcatattctcatagcagcagttttt--tttaataaatggcgttctgtaacctatcctcttggtttctttttgcag
|||| || ||||  |||      || || |||||||||||||| ||| |||||||||||||||||||||  ||||||||   | | | | | |   | |   | || | | | | ||     |  | |     | ||||| |||
CATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGCCTGATATCTTTAGgttggcaatattctctctgtacctgctatctgtctctcatatagtgctttttacttatttttatcttcgttttttttcag
















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|67020152|gb|CO448901.1|CO448901
EST:     GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG                         GGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAG
genomic: GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggtcata ... ctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAG
EST: gi|7145135|gb|AW506616.1|AW506616
EST:     GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG                         GGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAG
genomic: GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggtcata ... ctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAG
EST: gi|71430775|gb|DR811825.1|DR811825
EST:     GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG                         GGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAG
genomic: GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggtcata ... ctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAG
EST: gi|67043197|gb|CO469452.1|CO469452
EST:     GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG                         GGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAG
genomic: GAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggtcata ... ctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAG

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 587

CATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggtcata ... ctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

CATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggtcata ... ctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 389

CATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggtcata ... ctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 380

CATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAGgttggtcata ... ctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATT