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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtccttttacacaccatgacaactaaaatatttggtttagttttagtaaaactgagagagttttttttgtctaagtctatcgacacatgtaaatactagtactcagttttgttgtaaccatgcag

Basic information

species Zea mays
transcript GRMZM2G178460_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178460_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g16040.1 (Oryza sativa), 5'ss of exon 9
GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtccttttacacaccatgacaactaaaatatttggtttagttt-tagtaaaactgagagagttttttttgtctaagtctatcgacacatgtaaatactagtactcagttttgttgtaaccatgcag
|||||||||| ||||| ||||||| ||| || || ||||||||||| |||||||| |||||||||||||||||||||||||   |  | ||   |||  ||      ||  ||| |  || | ||| | | || ||||| ||    |  | ||| ||     | ||  || | | | | ||    | |||| ||  |  | ||||||||
GCATTGTGGAACGTGATGGTCTAATTGGACTATACAGAGGTTTTGTTCCAAATGCATTAAAAAATCTACCAAATAGCAGgtgccttttctttt-cacagtggtggtcaac-tatatatttaaatttatggcaacactgataggtaatagtatgtttactggca-cgtaacttctcattgct----cacagtattcctcaatccatgcag
















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|71423587|gb|DR806089.1|DR806089
EST:     CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG                         CATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
genomic: CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
EST: gi|50334119|gb|CO529245.1|CO529245
EST:     CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG                         CATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
genomic: CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
EST: gi|76919948|gb|DV167935.1|DV167935
EST:     CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG                         CATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGTTACTGGGCA
genomic: CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
EST: gi|32867170|gb|CF006852.1|CF006852
EST:     CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG                         CATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
genomic: CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
EST: gi|60397321|gb|DN230137.1|DN230137
EST:     CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG                         CATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
genomic: CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
EST: gi|74236987|gb|DT644901.1|DT644901
EST:     CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG                         CATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
genomic: CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
EST: gi|50333771|gb|CO528897.1|CO528897
EST:     ACCAAATAGCAG                         CATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
genomic: ACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
EST: gi|60397862|gb|DN230678.1|DN230678
EST:     CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG                         CATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
genomic: CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
EST: gi|213170460|gb|FM192673.1|FM192673
EST:     CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG                         CATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
genomic: CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
EST: gi|149004776|gb|EE039273.2|EE039273
EST:     CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG                         CATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
genomic: CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
EST: gi|71302052|gb|DR787104.1|DR787104
EST:     GTTTTGT-CCAAAATGCGTTAAAAAATCTACCAAATAGCAG                         CATTAAACTGACCGTTTTTGACACGGTGAAGACAATGATAGCTACTGGGCA
genomic: GTTTTGTGCC-AAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
EST: gi|74236988|gb|DT644902.1|DT644902
EST:     CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG                         CATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
genomic: CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
EST: gi|91872024|gb|EB401981.1|EB401981
EST:     ATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG                         CATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
genomic: ATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
EST: gi|110951541|gb|EE171593.1|EE171593
EST:     CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAG                         CATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA
genomic: CTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCA

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: 48 (upstream exon), 48 (downstream exon)
Score: 50

GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCAGAAGGAGATGGACAAATTAATTCAAGAAAATGAGGAGAAAAGAAGCTAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 89

GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCAGAAGGAGATGGACAAATTAATTCAAGAAAATGAGGAGAAAAGAAGCTAG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 62

GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCAGAAGGAGATGGACAAATTAATTCAAGAAAATGAGGAGAAAAGAAGCTAG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 62

GCATTGTGGAGCGTGACGGTCTAACTGGTCTTTATAGAGGTTTTGTGCCAAATGCGTTAAAAAATCTACCAAATAGCAGgtatgtcctt ... aaccatgcagCATTAAACTGACCGTGTTTGACACGGTGAAGACACTGATAGCTACTGGGCAGAAGGAGATGGACAAATTAATTCAAGAAAATGAGGAGAAAAGAAGCTAG