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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcatctgcctattccattcattcatatttccatttaatgctgcaacattctaactacaactgaatttattgtttggtgtagGTTGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCTATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG

Basic information

species Zea mays
transcript GRMZM2G068755_T03
intron # 28
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 28
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 29
gtatgtttca--tctgcctattccattcattcatatttccatttaatgctgcaacattctaactacaactgaatttattgtttggtgtagGTTGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCTATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG
||||| |  |    |  || ||   || | ||   | || | ||  |   | ||| ||    ||   ||||| |   |  ||    ||||||||  | ||||||||||||||||||||||||||||||||| |||||| ||||  || | |||||||| |||||||| ||||
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|32931347|gb|CF036159.1|CF036159
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTG                         GTTGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCTATTGTATCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggtgtagGTTGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCTATTGTATCA
EST: gi|32932391|gb|CF037203.1|CF037203
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTG                         GTTGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCTATTGTATCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggtgtagGTTGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCTATTGTATCA

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: 167

GATAAATCTTCTGAAGTCCGCAAAGCTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggtgtagGTTGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCTATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

GATAAATCTTCTGAAGTCCGCAAAGCTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggtgtagGTTGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCTATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

GATAAATCTTCTGAAGTCCGCAAAGCTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggtgtagGTTGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCTATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107

GATAAATCTTCTGAAGTCCGCAAAGCTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggtgtagGTTGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCTATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccatttaatgctgcaacattctaactacaactgaatttattgtttggtgtagGTTGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCTATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG
                     ttctaac  putative branch site (score: 107)
                                  tgaatttattgttt  TA-rich tract