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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtagtggtccacgaatatacatgttttttcagaccctctgcatgacagttgtttgttggtcatcctgtgtgctgcacctgagttgtgtgttatgatacagGTTCTTGCTGTTAAAAAGATAGATAGCGCCGCACTTTCTTTACAGGAAGAAGACAATTTCCTTGAGGCTGTATCGAGCATGTCTCGGCTAAGGCATCCAA

Basic information

species Zea mays
transcript GRMZM2G103070_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103070_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g09740.2 (Oryza sativa), 3'ss of exon 11
gtagtggtccacgaatatacatgttttttcagaccctctgcatgacagttgtttgttggtcatcctgtgtgctgcacctgagttgtgtgttatgat-acagGTTCTTGCTGTTAAAAAGATAGATAGCGCCGCACTTTCTTTACAGGAAGAAGACAATTTCCTTGAGGCTGTATCGAGCATGTCTCGGCTAAGGCATCCAA
    | | |    ||  || |  | |||  |     |   |       || ||| |  ||||| || ||  ||||  |||||||| ||| | ||||  ||||||||||| ||||| |||||||||||  | || ||||| || ||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||
-ctataggcagtaaaactaaaaatatttgaaattttttcaccctcttattatttttgtgtcatgctatgcactgcgactgagttgcgtgctgtgattgcagGTTCTTGCAGTTAAGAAGATAGATAGTTCAGCCCTTTCCTTGCAGGAAGAAGACAATTTTCTTGAGGCTGTATCGAGCATGTCACGGCTAAGGCATCCAA

upper sequence: GRMZM2G103070_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv10s0116g00100.t01 (Vitis vinifera), 3'ss of exon 11
-gtagtggtccacgaatatacatgttttttcagaccctctgcatgacagttgtttgttggtcatcctgtgtgctgcacctgagttgtgtgttatgatacagGTTCTTGCTGTTAAAAAGATAGATAGCGCCGCACTTTCTTTACAGGAAGAAGACAATTTCCTTGAGGCTGTATCGAGCATGTCTCGGCTAAGGCATCCAA
  ||    |   |    ||   ||  | |    |     | | | |   || | || |   |    |  ||        | |||  | || | ||||  ||    | ||  |||| |||||||| |  || ||||| |||||||| |||||||| ||||| ||||||||||| || |  ||||| || || ||||| | ||
gataccattttgcttggatggttggatctctgcagttgtttcttta-gcttatatgatatcccagataagtaacaatgtttagtcatctgatttgatctagACAATGGCAATTAAGAAGATAGACAATGCAGCACTGTCTTTACAAGAAGAAGATAATTTTCTTGAGGCTGTTTCAAATATGTCCCGTCTGAGGCACCAAA
















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|91868538|gb|EB400066.1|EB400066
EST:     GTGAGGGCTCACTTGGTCGTGTTTATAAGGCCGATTTCCCGAATGGAAAG                         GTTCTTGCTGTTAAAA-GATAGATAGCGCCGCACTT
genomic: GTGAGGGCTCACTTGGTCGTGTTTATAAGGCCGATTTCCCGAATGGAAAGgtacagtgtg ... tatgatacagGTTCTTGCTGTTAAAAAGATAGATAGCGCCGCACTT




















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: 49 (upstream exon), 49 (downstream exon)
Score: 203

CGCTTCTCTCCAAGTTGCTACTAATAGTTTCTGTCAAGATTCTCTTCTGGGTGAGGGCTCACTTGGTCGTGTTTATAAGGCCGATTTCCCGAATGGAAAGgtacagtgtg ... tatgatacagGTTCTTGCTGTTAAAAAGATAGATAGCGCCGCACTTTCTTTACAGGAAGAAGACAATTTCCTTGAGGCTGTATCGAGCATGTCTCGGCTAAGGCATCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

CGCTTCTCTCCAAGTTGCTACTAATAGTTTCTGTCAAGATTCTCTTCTGGGTGAGGGCTCACTTGGTCGTGTTTATAAGGCCGATTTCCCGAATGGAAAGgtacagtgtg ... tatgatacagGTTCTTGCTGTTAAAAAGATAGATAGCGCCGCACTTTCTTTACAGGAAGAAGACAATTTCCTTGAGGCTGTATCGAGCATGTCTCGGCTAAGGCATCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

CGCTTCTCTCCAAGTTGCTACTAATAGTTTCTGTCAAGATTCTCTTCTGGGTGAGGGCTCACTTGGTCGTGTTTATAAGGCCGATTTCCCGAATGGAAAGgtacagtgtg ... tatgatacagGTTCTTGCTGTTAAAAAGATAGATAGCGCCGCACTTTCTTTACAGGAAGAAGACAATTTCCTTGAGGCTGTATCGAGCATGTCTCGGCTAAGGCATCCAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 297

CGCTTCTCTCCAAGTTGCTACTAATAGTTTCTGTCAAGATTCTCTTCTGGGTGAGGGCTCACTTGGTCGTGTTTATAAGGCCGATTTCCCGAATGGAAAGgtacagtgtg ... tatgatacagGTTCTTGCTGTTAAAAAGATAGATAGCGCCGCACTTTCTTTACAGGAAGAAGACAATTTCCTTGAGGCTGTATCGAGCATGTCTCGGCTAAGGCATCCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttgtttgttggtcatcctgtgtgctgcacctgagttgtgtgttatgatacagGTTCTTGCTGTTAAAAAGATAGATAGCGCCGCACTTTCTTTACAGGAAGAAGACAATTTCCTTGAGGCTGTATCGAGCATGTCTCGGCTAAGGCATCCAA
                                            ttatgata  TA-rich tract