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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGGTACAACTGAGGATAACTTAGGAGCAGCCTTGTGCAAGAAGCTTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAGgtaaatataaatcacttattgaaatactcttctggtcccttttagaaggcttaccgacaattttgtcaagtccattatagaaggcactccttaggcctgg...

Basic information

species Zea mays
transcript GRMZM2G381933_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G381933_T03 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g15490.3 (Oryza sativa), 5'ss of exon 8
GTTTGGTACAACTGAGGATAACTTAGGAGCAGCCTTGTGCAAGAAGCTTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAGgtaaatataaatcactt--attgaaatact-------cttctggtcccttttagaaggcttaccgacaattttg---tcaagtccattatagaaggcactccttaggcctgg---------------------------------------------
||| || |||  |||||||||  |||| |||| ||||||||||||||||||||||||||||||||| |||||||||||||||||||||  |||||| ||||  |||| | |  |  || |||||| |       | | | | | |  |  |   |||| | | | | ||     |   ||  | |||  ||   |||    |    ||                                              
GTTCGGCACAGTTGAGGATAAGCTAGGTGCAGGCTTGTGCAAGAAGCTTCATGCAATTGGCTGGCGAGTTTCTCATGTAGCAGTTGTTTCCAATGAAgtaag-ataagttaaatgaatcgaaatagttgtatgtcctataggctccatgtgggagcttgcagcctacttgcaactgctgtgaactatgcaatctacttgccaactttgccagttttctggcacataatatctaacagaaattattgttatgcag
















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|33285805|gb|CF075600.1|CF075600
EST:     TTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAG                         ATTGATTCTGTTGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG
genomic: TTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAGgtaaatataa ... ggccttgcagATTGATTCTGTTGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG
EST: gi|33097429|gb|CF057389.1|CF057389
EST:     TTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAG                         ATTGATTCTGTTGTTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG
genomic: TTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAGgtaaatataa ... ggccttgcagATTGATTCTGTTGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG
EST: gi|33285569|gb|CF075364.1|CF075364
EST:     TTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAG                         ATTGATTCTGTTGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG
genomic: TTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAGgtaaatataa ... ggccttgcagATTGATTCTGTTGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG
EST: gi|33770862|gb|CF273156.1|CF273156
EST:     TTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAG                         ATTGATTCTGTTGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG
genomic: TTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAGgtaaatataa ... ggccttgcagATTGATTCTGTTGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG
EST: gi|78087486|gb|DV515879.1|DV515879
EST:     TTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAG                         ATTGATTCTGTTGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG
genomic: TTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAGgtaaatataa ... ggccttgcagATTGATTCTGTTGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG
EST: gi|67023704|gb|CO452453.1|CO452453
EST:     TTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAG                         ATTGATTCTGTCGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG
genomic: TTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAGgtaaatataa ... ggccttgcagATTGATTCTGTTGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG

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: 47 (upstream exon), 48 (downstream exon)
Score: 101

GTTTGGTACAACTGAGGATAACTTAGGAGCAGCCTTGTGCAAGAAGCTTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAGgtaaatataa ... ggccttgcagATTGATTCTGTTGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 85

GTTTGGTACAACTGAGGATAACTTAGGAGCAGCCTTGTGCAAGAAGCTTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAGgtaaatataa ... ggccttgcagATTGATTCTGTTGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

GTTTGGTACAACTGAGGATAACTTAGGAGCAGCCTTGTGCAAGAAGCTTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAGgtaaatataa ... ggccttgcagATTGATTCTGTTGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 174

GTTTGGTACAACTGAGGATAACTTAGGAGCAGCCTTGTGCAAGAAGCTTCATGCAATTGGCTGGCGGGTTTCTCATGTAGCAGTTGTTCGCAATGAGgtaaatataa ... ggccttgcagATTGATTCTGTTGCTGAAGAAGTTGAACGTTGTAAATCTACTGATGACATG