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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcaatatattacactatatgtcattataataatcttctatataaattatattaccaggatcttcctaatgatgacaatcattgtgtatggtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCTTGAGAAGGCATATGAAATTATATCCAATACAAAAGGGATTAATATCAAG

Basic information

species Zea mays
transcript GRMZM2G032944_T02
intron # 2
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|37417157|gb|CF646231.1|CF646231
EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGT
EST: gi|93284543|gb|EB676807.1|EB676807
EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
EST: gi|71765663|gb|DR963600.1|DR963600
EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
EST: gi|78116629|gb|DV535016.1|DV535016
EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
EST: gi|78124012|gb|DV542396.1|DV542396
EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
EST: gi|91047980|gb|EB158398.1|EB158398
EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
EST: gi|149085005|gb|EE174515.2|EE174515
EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
EST: gi|71448268|gb|DR829318.1|DR829318
EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
EST: gi|76014696|gb|DT941866.1|DT941866
EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
EST: gi|93284224|gb|EB676488.1|EB676488
EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
EST: gi|76914812|gb|DV165698.1|DV165698
EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
EST: gi|31355055|gb|CD439412.1|CD439412
EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
EST: gi|71438631|gb|DR819681.1|DR819681
EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
EST: gi|89761751|gb|DY689640.1|DY689640
EST:     GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACG                         GTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT
genomic: GTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCT

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: 47 (upstream exon), 42 (downstream exon)
Score: 44

ATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGATCATGCCAAGGTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCTTGAGAAGGCATATGAAATTATATCCAATACAAAAGGGATTAATATCAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 49

ATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGATCATGCCAAGGTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCTTGAGAAGGCATATGAAATTATATCCAATACAAAAGGGATTAATATCAAG


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 44

ATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGATCATGCCAAGGTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCTTGAGAAGGCATATGAAATTATATCCAATACAAAAGGGATTAATATCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 23

ATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGATCATGCCAAGGTTTTAGAAGTGGGGTGTGGGAATGGAAGCACTGCTGTTTCCATTCTACGgtaatgccct ... gtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCTTGAGAAGGCATATGAAATTATATCCAATACAAAAGGGATTAATATCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatattaccaggatcttcctaatgatgacaatcattgtgtatggtttcttcagGTCTAGTGAAAGGATCACTGTCTTTGCTTGTGACTGTAGTAAAGACACTCTTGAGAAGGCATATGAAATTATATCCAATACAAAAGGGATTAATATCAAG
                  tcctaat  putative branch site (score: 23)
                                              tttcttc  putative PPT
                     taatgat  TA-rich tract