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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaattttttgtctccaatttatgtttgtttttaatttcattatataaattctttgaatactcatcttgcttggtgtatcatcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTTGGCTTTGCTTACATTGGTGCAAAAGCACCAGGAGGGGGTGCAGTTG

Basic information

species Zea mays
transcript GRMZM2G047564_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047564_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g39344.2 (Oryza sativa), 3'ss of exon 4
--------gcaattttt-tgtctccaatttatgttt-gtttttaatttcattatataaattctttgaat------actcatcttgcttg-gtgtatcatcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTTGGCTTTGCTTACATTGGTGCAAAAGCACCAGGAGGGGGTGCAGTTG
        | ||||| | |  |||  |||||  |||  | || |   |   |||    | | |||||||       ||||   || | |  || |  |   || ||||| || ||||| || ||||| ||||||||||||||| ||||||| || ||||||||||||||||||||||| ||||| |||||||| ||||| ||||
gcaagtttgaaatttctgtaactctgatttagattttatgttcatcatttgtattctcagtatttgaattgtaaggctcaaaatgttcgcatgcactactgttacagAGGACGCTCCTGGCTATGCCAGAAAATGGTATTGGCTTGTTCCCGGACGTTGGCTTTGCTTACATTGGTGCCAAAGCTCCAGGAGGTGGTGCTGTTG

upper sequence: GRMZM2G047564_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv11s0016g04290.t01 (Vitis vinifera), 3'ss of exon 6
--gcaattttttgtctccaatttatgtttgtttt-taatttca-ttatataaattctttgaatactcatcttgcttggtgtatcatcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTTGGCTTTGCTTACATTGGTGCAAAAGCACCAGGAGGGGGTGCAGTTG
    |||            |  ||  ||||||||  || |||| ||| |  |||  | | | | || || ||  || ||      |  || |||||||| || || |||||||| |||||||| |||||| |||| ||||||||||| ||||||||||| |  ||| |    |||||||  ||  ||||||
gtataatggccatatatggacataaatttgttttgcaacttcaattagaataatgttctaatttctgatatttatttgtactaatttgtttcagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTTGGATTTGCTTACATAGCAGCACAGAGTCCAGGAGAAGGATCAGTTG
















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|149055220|gb|EE156145.2|EE156145
EST:     GATTTGGAATTGGGCTATCAGGGCATGGCCGCTACCGCATTATTACAGAG                         AGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTT
genomic: GATTTGGAATTGGGCTATCAGGGCATGGCCGCTACCGCATTATTACAGAGgcaatttttt ... atcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTT




















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 2 RNA-Seq libraries.


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 2

ACATGAGTATGCAAAACCTTATATATGCTTGATGGATGGAGTGACAATGGGATTTGGAATTGGGCTATCAGGGCATGGCCGCTACCGCATTATTACAGAGgcaatttttt ... atcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTTGGCTTTGCTTACATTGGTGCAAAAGCACCAGGAGGGGGTGCAGTTG


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 2

ACATGAGTATGCAAAACCTTATATATGCTTGATGGATGGAGTGACAATGGGATTTGGAATTGGGCTATCAGGGCATGGCCGCTACCGCATTATTACAGAGgcaatttttt ... atcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTTGGCTTTGCTTACATTGGTGCAAAAGCACCAGGAGGGGGTGCAGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcattatataaattctttgaatactcatcttgcttggtgtatcatcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTTGGCTTTGCTTACATTGGTGCAAAAGCACCAGGAGGGGGTGCAGTTG
     ttatataaattctttg  TA-rich tract