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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcatccacctattactttcattcatctttccatttaatgctgcagcattctcccaacaactgaatttattgtttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG

Basic information

species Zea mays
transcript GRMZM2G009849_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 29
gtatgtttca--tccacctattactttcattcatctttccatttaatgctgcagcattctcccaacaactgaatttattgtttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG
||||| |  |     | || ||| ||| | ||  || || | ||  |   | | | ||  | |    ||||| |   |  ||    |||||| |  | |||||||||||||||||||||||||||||||||||||||| ||||  || | |||||||| |||||||| ||||
gtatggtgtaatcttatcttttatttttactcgcctgtctactt--ttaagaaacttttcctctcttactga-tacgtcattgatggtagGTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCAGAGCGGTTAAAACTGTCCACTGTACACGAAG
















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|17970269|gb|BM277032.1|BM277032
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTG                         GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
EST: gi|22491327|gb|BU051250.1|BU051250
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTG                         GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
EST: gi|19351752|gb|BM896284.1|BM896284
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTG                         GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
EST: gi|32806646|gb|CD958880.1|CD958880
EST:     GATCTGTGGCCAAGAAGTG                         GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
genomic: GATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
EST: gi|87153866|gb|DY398655.1|DY398655
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTG                         GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
EST: gi|22489504|gb|BU049427.1|BU049427
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTG                         GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
EST: gi|87153811|gb|DY398600.1|DY398600
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTG                         GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA

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), 47 (downstream exon)
Score: 137

GATAAATCTTCTGAAGTCCGCAAAGCTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 16

GATAAATCTTCTGAAGTCCGCAAAGCTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 25

GATAAATCTTCTGAAGTCCGCAAAGCTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

GATAAATCTTCTGAAGTCCGCAAAGCTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccatttaatgctgcagcattctcccaacaactgaatttattgtttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG
     atttaat  putative branch site (score: 90)
                                  tgaatttattgttt  TA-rich tract