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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACATAAGGGGGAACAATCTCACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCTgtatgttggttctggcgattctgttggtgctttggttctccctagtttagtaggatgctatgatgcgaatttttctttgtatctggcatgcag

Basic information

species Zea mays
transcript GRMZM2G082855_T03
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082855_T03 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g03970.1 (Oryza sativa), 5'ss of exon 8
TGACATAAGGGGGAACAATCTCACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCTgtatgttggttctggcgattctgttggtgctttggttctccctagtttagtaggatgctatgatgcgaatttttctttgtatctggcatgcag
|||  ||||||| |||||||||||||| || ||||||||| |||||||||||||||| |||||||||||||||||||||  | ||   ||||    |  |  ||  ||  ||   |||||     ||  | || |||||| ||| |     ||| ||   |||||
TGATGTAAGGGGAAACAATCTCACAGGGACCATTCCAGAGAGCATAGGGAACTGCACCAGCTTTGAGATTCTgtatgttcttgctaa-gatttcagtaatatttcagtgttcatgagtttca---gacaccataatgcgagtttct-----tatttgtattgcag
















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|86472326|gb|DY238696.1|DY238696
EST:     ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCT                         GGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
genomic: ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCTgtatgttggt ... tggcatgcagGGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
EST: gi|148934014|gb|EC878019.2|EC878019
EST:     ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCT                         GGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
genomic: ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCTgtatgttggt ... tggcatgcagGGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
EST: gi|148940443|gb|EC885241.2|EC885241
EST:     ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCT                         GGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
genomic: ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCTgtatgttggt ... tggcatgcagGGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
EST: gi|149079906|gb|EE168912.2|EE168912
EST:     ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCT                         GGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
genomic: ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCTgtatgttggt ... tggcatgcagGGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
EST: gi|148964982|gb|EC906062.2|EC906062
EST:     ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCT                         GGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
genomic: ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCTgtatgttggt ... tggcatgcagGGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
EST: gi|148941048|gb|EC885905.2|EC885905
EST:     ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCT                         GGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
genomic: ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCTgtatgttggt ... tggcatgcagGGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
EST: gi|101383199|gb|EB813654.1|EB813654
EST:     ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCT                         GGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
genomic: ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCTgtatgttggt ... tggcatgcagGGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
EST: gi|148957491|gb|EC903572.2|EC903572
EST:     ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCT                         GGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA
genomic: ACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCTgtatgttggt ... tggcatgcagGGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 543

TGACATAAGGGGGAACAATCTCACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCTgtatgttggt ... tggcatgcagGGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

TGACATAAGGGGGAACAATCTCACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCTgtatgttggt ... tggcatgcagGGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 390

TGACATAAGGGGGAACAATCTCACAGGAACAATTCCAGAGGGCATAGGGAACTGCACTAGCTTTGAGATTCTgtatgttggt ... tggcatgcagGGATATTTCATACAACCAAATCTCTGGAGAAATACCATACAACATAGGTTACCTTCAAGTAGCCACACT