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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagagatactatatcttacagctaccaaaccgatcgcccatcgcaagcagcacgcgtctcgctcgggaacgaattaatcctggtcgatcccatggcgcgtttggtcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAACCGGGGGGCCACGCGCTCCGCGTCCATCACCGCGGCATGGCCGGACGTGG

Basic information

species Zea mays
transcript GRMZM2G146463_T03
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146463_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os07g26900.1 (Oryza sativa), 3'ss of exon 12
gtacagagatactatatcttacagctaccaaaccgatcgcccatcgcaagcagcacgcgtctcgctcgggaacgaattaatcctggtcgatcccatggcgcgtttggtcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAACCGGGGGGCCACGCGCTCCGCGTCCATCACCGCGGCATGGCCGGACGTGG
              | |    ||  ||  | | | |   || |     | || ||    | ||  ||   |   |||          |||||      | | | |  ||   | |||||||||||||||| ||||||   ||| |||| ||||||||||||||| ||||| || |||||| ||  |  |   ||||| ||||| |||| |||| | |
-------------gtgtgcagca-ttattatagctactaccaaaaatcatcaacagat-tttcattccaaactaaatcg--------cgatcttgaatcacatct--tc--ctacagGTATGGGCAGGGCCGCTCTCCCAGCAGAGGACGGCGGTGCTGCTGCTGAACCGCGGCGCCACGGGCAGCCGGCAGATCACGGCGGCGTGGCAGGACATCG
















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|71443279|gb|DR824329.1|DR824329
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|86465787|gb|DY232160.1|DY232160
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|78113278|gb|DV531670.1|DV531670
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|86466262|gb|DY232634.1|DY232634
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|5006127|gb|AI712189.1|AI712189
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|71443417|gb|DR824467.1|DR824467
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|50334851|gb|CO529977.1|CO529977
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|60357458|gb|DN224431.1|DN224431
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|87157241|gb|DY402030.1|DY402030
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACNGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|91874598|gb|EB404555.1|EB404555
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGTTGTTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|60338146|gb|DN205119.1|DN205119
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|74238711|gb|DT646625.1|DT646625
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|71318125|gb|DR795824.1|DR795824
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|91054334|gb|EB164752.1|EB164752
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|89763955|gb|DY690933.1|DY690933
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|149055655|gb|EE156360.2|EE156360
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|78080807|gb|DV509219.1|DV509219
EST:     GGGTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|71430639|gb|DR811689.1|DR811689
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|50330298|gb|CO525424.1|CO525424
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|78073768|gb|DV502202.1|DV502202
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|78075208|gb|DV503642.1|DV503642
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATTTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGTTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|87156914|gb|DY401703.1|DY401703
EST:     GGCTGGGTGTCCA-GGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCT
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCT
EST: gi|211420211|gb|FL465092.1|FL465092
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGTTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|78088430|gb|DV516823.1|DV516823
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|89763171|gb|DY690487.1|DY690487
EST:     GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAG                         GTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGTTGCTGTTCAAC
genomic: GGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC
EST: gi|60353667|gb|DN220640.1|DN220640
EST:     GCAACGATCTCGAG                         GTATGGGCAGGGCAGCTATAGGGACACAGGAAGGCGGTGCAGCTGCTCAAC
genomic: GCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAAC

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: 43 (upstream exon), 48 (downstream exon)
Score: 40

ATCGGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAACCGGGGGGCCACGCGCTCCGCGTCCATCACCGCGGCATGGCCGGACGTGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 22

ATCGGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAACCGGGGGGCCACGCGCTCCGCGTCCATCACCGCGGCATGGCCGGACGTGG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 6

ATCGGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAACCGGGGGGCCACGCGCTCCGCGTCCATCACCGCGGCATGGCCGGACGTGG


Block sizes: 40 (upstream exon), 10 (downstream exon)
Score: 1

ATCGGCTGGGTGTCCAAGGACAGAAAGTGAGCAAGTACGGCAACGATCTCGAGgtacagagat ... tcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAACCGGGGGGCCACGCGCTCCGCGTCCATCACCGCGGCATGGCCGGACGTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctcgggaacgaattaatcctggtcgatcccatggcgcgtttggtcaattgcagGTATGGGCAGGGCAGCTCTCGGGGCACAGGAAGGCGGTGCTGCTGCTCAACCGGGGGGCCACGCGCTCCGCGTCCATCACCGCGGCATGGCCGGACGTGG
            aattaat  putative branch site (score: 1)
            aattaat  TA-rich tract