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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggtgagctgttctcgtcatttcgatgctagtaccattatattgttgttgttgtcagcaatgacgagaatgatccaggctaatttaaagcaaagcgatccatgaactggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACGATCGACCTCAAGAGCGCCATCAAGTACCACCGGAACCTGACGTCCAGAG

Basic information

species Zea mays
transcript GRMZM2G471269_T04
intron # 10
splice site 3'
intron type U2

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|71762617|gb|DR960554.1|DR960554
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|5108189|gb|AI739902.1|AI739902
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|78027468|gb|DV495855.1|DV495855
EST:     TGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: TGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|78120814|gb|DV539198.1|DV539198
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|148949256|gb|EC894699.2|EC894699
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|14203015|gb|BG836692.1|BG836692
EST:     ATTTCTGGGCGAACGATGAACGMACTCGMACAGCTCTTGGGATCAAGAAG                         GGMACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGMCCTGCCGTAMACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|78083939|gb|DV512332.1|DV512332
EST:     ATTTTTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|211231289|gb|FL464293.1|FL464293
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|88750452|gb|DY534593.1|DY534593
EST:     GAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: GAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|5069690|gb|AI737655.1|AI737655
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|8401242|gb|BE056876.1|BE056876
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|71299116|gb|DR785562.1|DR785562
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTTTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|211175969|gb|FL481229.1|FL481229
EST:     ACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|74233921|gb|DT641835.1|DT641835
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|110516814|gb|EE021401.1|EE021401
EST:     CACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: CACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|78026574|gb|DV494961.1|DV494961
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|78125073|gb|DV543457.1|DV543457
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|148966524|gb|EE017546.2|EE017546
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|67026269|gb|CO455018.1|CO455018
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGCCACAACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|37397736|gb|CF636176.1|CF636176
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
EST: gi|40337181|gb|CK371251.1|CK371251
EST:     ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAG                         GGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG
genomic: ATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACG

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), 48 (downstream exon)
Score: 23

ACCTACGGCTACTACCTGTCGTATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACGATCGACCTCAAGAGCGCCATCAAGTACCACCGGAACCTGACGTCCAGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 100

ACCTACGGCTACTACCTGTCGTATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACGATCGACCTCAAGAGCGCCATCAAGTACCACCGGAACCTGACGTCCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

ACCTACGGCTACTACCTGTCGTATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACGATCGACCTCAAGAGCGCCATCAAGTACCACCGGAACCTGACGTCCAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 104

ACCTACGGCTACTACCTGTCGTATTTCTGGGCGAACGATGAACGCACTCGAACAGCTCTTGGGATCAAGAAGgtacggtgag ... tggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACGATCGACCTCAAGAGCGCCATCAAGTACCACCGGAACCTGACGTCCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacgagaatgatccaggctaatttaaagcaaagcgatccatgaactggtggtcagGGAACAGTGGACGAGTGGGTGAGGTGTCACGACGCAGACCTGCCGTACACGATCGACCTCAAGAGCGCCATCAAGTACCACCGGAACCTGACGTCCAGAG
               ggctaat  putative branch site (score: 104)
                  taatttaaagcaaa  TA-rich tract