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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcaggaattctcatctctactttgctgttatatctttctgaagtgctacttaatcattagtggttttttcagtgtgcacttttctgtctttcaatcagaactctctgtattcatatgaatcttcttttctgcccgaagaaaaaaaagtgatgatagtatccaaactctgtagATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGTCAAACAATGAATTGCCAAATGGCCAATTGGGAAGCTTGCAACCTCTCCC

Basic information

species Zea mays
transcript GRMZM2G062953_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062953_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 9
gtatgtcaggaattctcatctctactttgctgttatatctttctgaagtgctacttaatcattagtggttttttcagtgtgcacttttctgtctttcaa--tcagaactctctgtattcatatgaatcttcttttctgcccgaagaaaaaaaagtgatgatagtatccaaactctgtagATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGTCAAACAATGAATTGCCAAATGGCCAATTGGGAAGCTTGCAACCTCTCCC-
                           |  ||  || | ||| |  | |   | ||    |       ||||| |        | |  || || ||  |  |||||||      | | |||     | |||| || ||  |   ||| |||   |||||    |  |  || | ||||||||| |||||||||  |||||| || ||||||||||| |||||| ||||| ||| |   ||  || ||||||||   |  | |  ||  |    | ||   
--------------------------gtattgcaatttatttatacatttacatttctcaacc-----tttttcctacaccatcatccctatcattggatgtcagaaccacgcatgtccatgcttgtgttctgtt-tgagctttgaagaaattctgatgggtct-cctgaattttgtagATGAGCAAAGTGGAGCCCTTCCCCCACCTCCTTGGGAAGCTCAGTCAGCGCCAAGCGGCGACATGTCAAATGGC-GGTATGCAGTCTCACCCGGTGTCAAA
















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|86472480|gb|DY238850.1|DY238850
EST:     TCAAGCTGCCAACCCTGTTGTGCCCCTGCCAGAGCAAGCACTGAATTACG                         ATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCACCCAGCGT
genomic: TCAAGCTGCCAACCCTGTTGTGCCCCTGCCAGAGCAAGCACTGAATTACGgtatgtcagg ... aactctgtagATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGT
EST: gi|19821886|gb|BQ047910.1|BQ047910
EST:     TCAAGCTGCCAACCCTGCTGTGCCCCTGCCAGAGCAAGCACTGAATTACG                         ATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGT
genomic: TCAAGCTGCCAACCCTGTTGTGCCCCTGCCAGAGCAAGCACTGAATTACGgtatgtcagg ... aactctgtagATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGT
EST: gi|30160651|gb|CB924380.1|CB924380
EST:     TCAAGCTGCCAACCCTGTTGTGCCCCTGCCAGAGCAAGCACTGAATTACG                         ATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGT
genomic: TCAAGCTGCCAACCCTGTTGTGCCCCTGCCAGAGCAAGCACTGAATTACGgtatgtcagg ... aactctgtagATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGT
EST: gi|71764440|gb|DR962377.1|DR962377
EST:     TCAAGCTGCCAACCCTGTTGTGCCCCTGCCAGAGCAAGCACTGAATTACG                         ATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGT
genomic: TCAAGCTGCCAACCCTGTTGTGCCCCTGCCAGAGCAAGCACTGAATTACGgtatgtcagg ... aactctgtagATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGT
EST: gi|71438882|gb|DR819932.1|DR819932
EST:     TCAAGCTGCCAACCCTGTTGTGCCCCTGCCAGAGCAAGCACTGAATTACG                         ATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGT
genomic: TCAAGCTGCCAACCCTGTTGTGCCCCTGCCAGAGCAAGCACTGAATTACGgtatgtcagg ... aactctgtagATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGT

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), 48 (downstream exon)
Score: 93

TCTTACGATCAGGCATCCCAGTTTAAAAATGTTAGTTCTGGGTGGAATGGTCAAGCTGCCAACCCTGTTGTGCCCCTGCCAGAGCAAGCACTGAATTACGgtatgtcagg ... aactctgtagATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGTCAAACAATGAATTGCCAAATGGCCAATTGGGAAGCTTGCAACCTCTCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 246

TCTTACGATCAGGCATCCCAGTTTAAAAATGTTAGTTCTGGGTGGAATGGTCAAGCTGCCAACCCTGTTGTGCCCCTGCCAGAGCAAGCACTGAATTACGgtatgtcagg ... aactctgtagATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGTCAAACAATGAATTGCCAAATGGCCAATTGGGAAGCTTGCAACCTCTCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

TCTTACGATCAGGCATCCCAGTTTAAAAATGTTAGTTCTGGGTGGAATGGTCAAGCTGCCAACCCTGTTGTGCCCCTGCCAGAGCAAGCACTGAATTACGgtatgtcagg ... aactctgtagATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGTCAAACAATGAATTGCCAAATGGCCAATTGGGAAGCTTGCAACCTCTCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

TCTTACGATCAGGCATCCCAGTTTAAAAATGTTAGTTCTGGGTGGAATGGTCAAGCTGCCAACCCTGTTGTGCCCCTGCCAGAGCAAGCACTGAATTACGgtatgtcagg ... aactctgtagATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGTCAAACAATGAATTGCCAAATGGCCAATTGGGAAGCTTGCAACCTCTCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcttcttttctgcccgaagaaaaaaaagtgatgatagtatccaaactctgtagATGATCAAAGTGGAAACCTTCCACCGCCTCCTTGGGAGGCTCAGCCAGCGTCAAACAATGAATTGCCAAATGGCCAATTGGGAAGCTTGCAACCTCTCCC
                  aagaaaaaaaa  TA-rich tract