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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatacaatcaaacttttctttgaagtgccatgctggcttagtaaccccttcattccagaatctgtttccgttgaaaaaactattcataattcaattgttctgatgtattttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAGAATTCCAGAAAAGATCTTGTAGTAGAAATTGATCCTGTCAATAATGAAA

Basic information

species Zea mays
transcript GRMZM2G130889_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130889_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 2
gtaaatacaatcaaacttttctttgaagtgccatgctggcttagtaaccccttcattccagaatctgtttccgttgaaaaaactattcataattcaattgttctgatgtattttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAGAATTCCAGAAAAGATCTTGTAGTAGAAATTGATCCTGTCAATAATGAAA------
            ||| |||  | |||| |||  |||||| ||| | | |  || || ||||          | || ||| || | ||                   ||| | ||  | || ||||||||||||||||| |||||||||||||||||  ||   |  | ||    |||||| || | |||||||   ||||||||||| | ||||||||||      
----------gtaaagtttgttctgaaatgcggtgctggtttacttaacttttaat-ccag----------ctttaaaataaatctt-------------------tgtttcttgtatagTTAAGAAAGGCTGGAGTTCATCTGGATGAAAATCCAACAG---GTGACAAAGTATCCAGAGAAAAGCTTGTAG---AAATTGATCCTATTAATAATGAAAGGAGAG
















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|148937008|gb|EC881178.2|EC881178
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|148934064|gb|EC878076.2|EC878076
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|149108157|gb|EE292504.2|EE292504
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|211506494|gb|FL158303.1|FL158303
EST:     TCTGAGATTTCGCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
genomic: TCTGAGATTTC-CCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|32929134|gb|CF033946.1|CF033946
EST:     AGTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCTGTAGTAAGCAACAAG
genomic: AGTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|211508842|gb|FL158306.1|FL158306
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|148930753|gb|EC873061.2|EC873061
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|19058210|gb|BM736877.1|BM736877
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAACAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|18964229|gb|BM660885.1|BM660885
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAACAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|20300875|gb|BQ163818.1|BQ163818
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAACAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|32929269|gb|CF034081.1|CF034081
EST:     AGTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCTGTAGTAAGCAACAAG
genomic: AGTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|20301029|gb|BQ163972.1|BQ163972
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAACAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|149073799|gb|EE162117.2|EE162117
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|87151942|gb|DY396731.1|DY396731
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAACAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|78112348|gb|DV530742.1|DV530742
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|20300848|gb|BQ163791.1|BQ163791
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAACAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|32928842|gb|CF033654.1|CF033654
EST:     AGTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAACAAG
genomic: AGTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|87153018|gb|DY397807.1|DY397807
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAACAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|19057740|gb|BM736407.1|BM736407
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAACAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|22490422|gb|BU050345.1|BU050345
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAACAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|32929345|gb|CF034157.1|CF034157
EST:     AGTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCATTATTAAGCAACAAG
genomic: AGTCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|18964227|gb|BM660884.1|BM660884
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAACAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAG
EST: gi|211506492|gb|FL158301.1|FL158301
EST:     TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAG                         CTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAG
genomic: TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAG

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), 47 (downstream exon)
Score: 157

TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAGAATTCCAGAAAAGATCTTGTAGTAGAAATTGATCCTGTCAATAATGAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 171

TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAGAATTCCAGAAAAGATCTTGTAGTAGAAATTGATCCTGTCAATAATGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 259

TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAGAATTCCAGAAAAGATCTTGTAGTAGAAATTGATCCTGTCAATAATGAAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 266

TCTGAGATTTCCCGATTAGAAGATGATATAAATCGGTTGCATGACCAGgtaaatacaa ... ttttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAGAATTCCAGAAAAGATCTTGTAGTAGAAATTGATCCTGTCAATAATGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttccgttgaaaaaactattcataattcaattgttctgatgtattttcaacagCTAAGAAAGGCTGGAGTTAATCTGGATGAAAATCCAGTAGTAAGCAATAAGAATTCCAGAAAAGATCTTGTAGTAGAAATTGATCCTGTCAATAATGAAA
                                   ttctgat  putative branch site (score: 266)
                                           tattttc  CT-rich tract
           aaaaaactattcataa  TA-rich tract