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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccttcagtatgatgaactcttgaaagttacgtcatcatgtacgtatgaaattttctctggctctgatcatgcatcatgagtgcagGCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATGCCATTCCTGGACCGGATCAATGCAATAGAGGGGCGGAAGGCGTATGCAA

Basic information

species Zea mays
transcript GRMZM2G017616_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017616_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g08220.1 (Oryza sativa), 3'ss of exon 6
gtaccttcagtatgatgaactcttgaaagttacgtcatcatgtacgtatgaaattttctctggctctgatcatgcatcatgagtgcagGCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATGCCATTCCTGGACCGGATCAATGCAATAGAGGGGCGGAAGGCGTATGCAA
||||| ||| | ||||||  |||| ||   |      |  ||| |  |||    ||  |||   ||||||||    |||  | || ||||  ||||||| ||||||||||||||| ||||||||||||| | |||  |||||||| |||||||||||||||| ||||| || ||||| || ||||| |
gtaccatcattttgatgaggtcttaaatcatgtccagtagtgtccccatgg---ttattct--ttctgatcacatgtcacaattgaagGCAATGGACGAAGCAAAGCTGTTCATAGTGGACTACCATGACGCATACCTGCCATTCTTGGACCGGATCAATGCGATAGATGGACGGAAAGCATATGCGA
















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|211506486|gb|FL158295.1|FL158295
EST:     TCACAGAAGCTCACATCACTGGACAGCTCAATGGACTCACAGTACAACAG                         GCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATCTG
genomic: TCACAGAAGCGCACATCACTGGACAGCTCAATGGACTCACGGTACAACAGgtaccttcag ... atgagtgcagGCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATG
EST: gi|211506485|gb|FL158294.1|FL158294
EST:     TCACAGAAGCTCACATCACTGGACAGCTCAATGGACTCACAGTACAACAG                         GCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATCTG
genomic: TCACAGAAGCGCACATCACTGGACAGCTCAATGGACTCACGGTACAACAGgtaccttcag ... atgagtgcagGCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATG
EST: gi|71315075|gb|DR794165.1|DR794165
EST:     TCACAGAAGCGCACATCACTGGACAGCTCAATGGACTCACGGTACAACAG                         GCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATG
genomic: TCACAGAAGCGCACATCACTGGACAGCTCAATGGACTCACGGTACAACAGgtaccttcag ... atgagtgcagGCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATG
EST: gi|211506487|gb|FL158296.1|FL158296
EST:     TCACAGAAGCTCACATCACTGGACAGCTCAATGGACTCACAGTACAACAG                         GCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATCTG
genomic: TCACAGAAGCGCACATCACTGGACAGCTCAATGGACTCACGGTACAACAGgtaccttcag ... atgagtgcagGCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATG
EST: gi|78103541|gb|DV521969.1|DV521969
EST:     TCACAGAAGCGCACATCACTGGACAGCTCAATGGACTCACGGTACAACAG                         GCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATG
genomic: TCACAGAAGCGCACATCACTGGACAGCTCAATGGACTCACGGTACAACAGgtaccttcag ... atgagtgcagGCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATG
EST: gi|32799354|gb|CD951590.1|CD951590
EST:     TCACAGAAGCGCACATCACTGGACAGCTCAATGGACTCACGGTACAACAG                         GCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATG
genomic: TCACAGAAGCGCACATCACTGGACAGCTCAATGGACTCACGGTACAACAGgtaccttcag ... atgagtgcagGCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATG

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

ACCAGTAAGCAAGATGGATCCTGCAATCTATGGCCCGCCAGAATCATCGATCACAGAAGCGCACATCACTGGACAGCTCAATGGACTCACGGTACAACAGgtaccttcag ... atgagtgcagGCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATGCCATTCCTGGACCGGATCAATGCAATAGAGGGGCGGAAGGCGTATGCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 82

ACCAGTAAGCAAGATGGATCCTGCAATCTATGGCCCGCCAGAATCATCGATCACAGAAGCGCACATCACTGGACAGCTCAATGGACTCACGGTACAACAGgtaccttcag ... atgagtgcagGCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATGCCATTCCTGGACCGGATCAATGCAATAGAGGGGCGGAAGGCGTATGCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 77

ACCAGTAAGCAAGATGGATCCTGCAATCTATGGCCCGCCAGAATCATCGATCACAGAAGCGCACATCACTGGACAGCTCAATGGACTCACGGTACAACAGgtaccttcag ... atgagtgcagGCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATGCCATTCCTGGACCGGATCAATGCAATAGAGGGGCGGAAGGCGTATGCAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 24

ACCAGTAAGCAAGATGGATCCTGCAATCTATGGCCCGCCAGAATCATCGATCACAGAAGCGCACATCACTGGACAGCTCAATGGACTCACGGTACAACAGgtaccttcag ... atgagtgcagGCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATGCCATTCCTGGACCGGATCAATGCAATAGAGGGGCGGAAGGCGTATGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcatcatgtacgtatgaaattttctctggctctgatcatgcatcatgagtgcagGCGGTGGACGAGGCAAAGCTGTTCATATTGGACTACCATGATGTATATATGCCATTCCTGGACCGGATCAATGCAATAGAGGGGCGGAAGGCGTATGCAA
                              ctctgat  putative branch site (score: 24)
             tatgaaatttt  TA-rich tract