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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatcagagatttattctagttttctgtgaaggatcttctatgttttaagtcatacaaattttgatgtttcccataatcctttgtggtgatgtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG

Basic information

species Zea mays
transcript GRMZM2G451716_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 11
gtatatatcagagatttattctagttttctgtgaaggatcttctatgttttaagtcatacaaattttgatgtttcccat--aatcctttgtggtgat----gtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG
      ||       |  || | |||||         |  | ||  | ||   ||   |     | | || | | || |   ||    | |  || |    ||||||| || ||||| |||||||| || || |||||||||  ||| || ||||||||||||||||| ||  ||||||||||||| || 
-----cattcatttctatttgtggttttacacaccataattgctcagattcctgttgcatcctctgttatttctgccttttgatttgatataatggtaattgtagGTATACTTCAAAAATGCTTCTTGCTGCAATTGATGAACATCATCGAGGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAA

upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv01s0150g00090.t01 (Vitis vinifera), 3'ss of exon 12
gtatatatcagag-atttattctagttttctgtgaaggatcttctatgttttaagtcatacaaattttgatgtttcccataatcctttgtggtgat-gtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG
   |  |  |||  |  | ||  || ||| | |    | | ||   ||       |  |     | ||  |  |||  ||  |   |  || | || | || || || |||||||||||| |||| || ||||||||| | |||||||| ||||| ||||| || ||||| || ||||| || |||
-actgcaatagaataaatctttcagatttgtttagttgttttttcttgaaacctcttcttgctttcttactagttctgattttgaatgatgataattgcagATATACTTCAAAGATGCTTTTGGCTGCAATTGATGAACGCCACCGGGGGACTTACGATTTCATTTACCTACCCATTGATTTCAAG
















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|78073984|gb|DV502418.1|DV502418
EST:     CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAA                         GTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC
genomic: CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAAgtatatatca ... ggtgatgtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC
EST: gi|5895966|gb|AW037212.1|AW037212
EST:     CGGNGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAA                         GTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC
genomic: CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAAgtatatatca ... ggtgatgtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC
EST: gi|5895962|gb|AW037208.1|AW037208
EST:     CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAA                         GTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAT
genomic: CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAAgtatatatca ... ggtgatgtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC
EST: gi|213191920|gb|FM183353.1|FM183353
EST:     CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAA                         GTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC
genomic: CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAAgtatatatca ... ggtgatgtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC
EST: gi|76928188|gb|DV171510.1|DV171510
EST:     CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAA                         GTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC
genomic: CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAAgtatatatca ... ggtgatgtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC
EST: gi|31358340|gb|CD442697.1|CD442697
EST:     CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAA                         GTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC
genomic: CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAAgtatatatca ... ggtgatgtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC
EST: gi|71301676|gb|DR786905.1|DR786905
EST:     CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAA                         GTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC
genomic: CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAAgtatatatca ... ggtgatgtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC
EST: gi|91048864|gb|EB159282.1|EB159282
EST:     CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAA                         GTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC
genomic: CGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAAgtatatatca ... ggtgatgtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAAC

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

ATCAATCTGACAACAAAAGGCTGTTTGAGCTTGACATTGAGCGTATAGTCCGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAAgtatatatca ... ggtgatgtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 128

ATCAATCTGACAACAAAAGGCTGTTTGAGCTTGACATTGAGCGTATAGTCCGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAAgtatatatca ... ggtgatgtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

ATCAATCTGACAACAAAAGGCTGTTTGAGCTTGACATTGAGCGTATAGTCCGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAAgtatatatca ... ggtgatgtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 64

ATCAATCTGACAACAAAAGGCTGTTTGAGCTTGACATTGAGCGTATAGTCCGGGGCGAGGACTCCCGGACTACACTGATGATAAAGAATATCCCAAACAAgtatatatca ... ggtgatgtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttttaagtcatacaaattttgatgtttcccataatcctttgtggtgatgtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG
                   ttttgat  putative branch site (score: 64)
            atacaaattttgat  TA-rich tract