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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagagcacatcgatcgatcatcggctcttgtcatcttcaacctccctccctccgtccgatccagtccactgcctaagaatccatccaactgcatgtctgatcatcgtcttgtatccatgacagGGCATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATAC

Basic information

species Zea mays
transcript GRMZM2G139372_T05
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139372_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g02820.1 (Oryza sativa), 3'ss of exon 4
gtaagcagagcacatcgatcgatcatcggctcttgtcatcttcaacctccctccctccgtccga-tccagtccactgcctaagaatccatc-caactgcatgtctgatcatcgtcttgtatccatgacagGGCATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATAC
                         |  ||     |||||    | | |  |  ||   || || ||     |     || |  ||  ||| |     |   |  | |      |||| || | || ||||    || | ||||| | |    | |||| ||| | | ||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||| 
------------------------gtaagcaagattcatcactgaacccagtagctgaatctgaatctgaatctgaatctgaatatgaatctctgtcactgatgaggtgtgttgcttggatgcgtggcagGA---GGAGGAGGAGGCTGATGGCGGCGGTGGCGCCAAGACGCGGCTGCTGGTCCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGTCGAGATAT
















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|149096501|gb|EE182246.2|EE182246
EST:     CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTG---                         G-CATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG
genomic: CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTGTACgtaagcagag ... tccatgacagGGCATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG
EST: gi|149099194|gb|EE185222.2|EE185222
EST:     CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTGTAC                         GGCATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG
genomic: CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTGTACgtaagcagag ... tccatgacagGGCATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG
EST: gi|149084417|gb|EE173872.2|EE173872
EST:     CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTG---                         G-CATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG
genomic: CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTGTACgtaagcagag ... tccatgacagGGCATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG
EST: gi|149090656|gb|EE179979.2|EE179979
EST:     CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTG---                         G-CATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGTGGACGCGGCTGCTG
genomic: CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTGTACgtaagcagag ... tccatgacagGGCATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG
EST: gi|148933084|gb|EE286018.2|EE286018
EST:     CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTG---                         G-CATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG
genomic: CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTGTACgtaagcagag ... tccatgacagGGCATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG
EST: gi|149103852|gb|EE289263.2|EE289263
EST:     CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTG---                         G-CATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG
genomic: CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTGTACgtaagcagag ... tccatgacagGGCATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG
EST: gi|149073865|gb|EE162188.2|EE162188
EST:     CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTG---                         G-CATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG
genomic: CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTGTACgtaagcagag ... tccatgacagGGCATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG
EST: gi|149071950|gb|EE160336.2|EE160336
EST:     CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTG---                         G-CATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG
genomic: CTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTGTACgtaagcagag ... tccatgacagGGCATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTG

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 1 RNA-Seqlibrary.


Block sizes: 14 (upstream exon), 36 (downstream exon)
Score: 2

GATGCACGCCGAGGCAATGGTGTCCAACCAGCCGATCTGGCAGAGCAGCCGCGTGCCAGAGCTCCAAACAGGTTACTCCAGTGTACgtaagcagag ... tccatgacagGGCATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcctaagaatccatccaactgcatgtctgatcatcgtcttgtatccatgacagGGCATGGTGCAGGAGCCCGGGTCCAGCGGCGGCCCGAGGACGCGGCTGCTGGTGCCCGTCGCCGGCGGCCTCGTCGAGCTCTTCGCGGCGAGATAC
                          gtctgat  putative branch site (score: 2)
     taagaat  TA-rich tract