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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgataacatactgcattatacttgaggaggctaatactttaacataagtattgaaccttgagtgcattacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGATATCGTTGTGGTTGGCATTAACATAACAACACAAGTCTGCCTGACAG

Basic information

species Zea mays
transcript GRMZM2G015344_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015344_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g44370.1 (Oryza sativa), 3'ss of exon 5
--------------gtatgataacatactgcattatacttgaggaggctaa-tactttaacataagtattgaaccttgagtgcattacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGATATCGTTGTGGTTGGCATTAACATAACAACACAAGTCTGCCTGACAG
              | ||  ||   || ||| || ||| ||   ||   || ||| || ||| ||||||| |   ||   ||||| || ||||||||  ||||||| |||||||||||||||||||||||||| |||||||||||| | |  ||||||||||||||||||||||| ||||||||  | ||||
gtaatgtcattattgcatattagactagtgc-ttgtacatggacagaaaaaatacattgacacaagtattaagttttcgctgcataactctgcagATATATGGAGATCCAGAAGCAGCTGACATAGTTTTTACCTCAGGAGCAGATGTTGACGTGGTTGGCATTAACATAACAACTCAAGTCTGTTTTACAG

upper sequence: GRMZM2G015344_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G35170.1 (Glycine max), 3'ss of exon 5
-----------------gtatg-ataacatactgcattatacttgaggaggctaatac-tttaacataagtattgaaccttgagtgcattacact-gcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGATATCGTTGTGGTTGGCATTAACATAACAACACAAGTCTGCCTGACAG
                   ||| ||  ||| ||    ||  ||  |  |    | | | ||| | ||  ||  |   ||    |   |||  ||| |||||||||||||||||| ||||| || || || || ||||| || || |||||||| |||||  |||| || ||||| ||||| ||||||    | ||||
tggtcgtaacggctaataaatggattccattctaggctaatctcaataatttgatttcatttcaaatgggtcctagtccaaatgactattctacttgcagATCCATGGAGACCCGGAAGCCGCAGATATTGTGTTTACCTCTGGGGCAGATATTGTTGTTATTGGAATAAACATTACAACCCAAGTCCAATTCACAG
















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|89759746|gb|DY688465.1|DY688465
EST:     GTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAAT                         ATCCATGGAGACCCAGAAGCAGCTGACATAGTTT
genomic: GTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTT
EST: gi|71318567|gb|DR796043.1|DR796043
EST:     GTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAAT                         ATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGC
genomic: GTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGC
EST: gi|71449461|gb|DR830511.1|DR830511
EST:     GTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAAT                         ATCCATGGAGACCCAGAAGCAGCTGACATAGTTT
genomic: GTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTT
EST: gi|76935894|gb|DV174515.1|DV174515
EST:     GTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAAT                         ATCCATGGAGACTCAGAAGCAGCTGACATAGTTTTTACT
genomic: GTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACT
EST: gi|76935893|gb|DV174514.1|DV174514
EST:     GAAATGTCAACCCTGCTGCTGAAGCAAAT                         ATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
genomic: GAAATGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
EST: gi|71759994|gb|DR957931.1|DR957931
EST:     GAAATGTCAACCCTGCTGCTGAAGCAAAT                         ATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
genomic: GAAATGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
EST: gi|71438819|gb|DR819869.1|DR819869
EST:     GTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAAT                         ATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
genomic: GTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
EST: gi|78105410|gb|DV523828.1|DV523828
EST:     GTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAAT                         ATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
genomic: GTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
EST: gi|71759693|gb|DR957630.1|DR957630
EST:     TGTCAACCCTGCTGCTGAAGCAAAT                         ATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
genomic: TGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
EST: gi|76290576|gb|DV030144.1|DV030144
EST:     GTGGAGCTTTCTTTGCGGCTGGGAATGTCAACCCTGCTGCTGAAGCAA-T                         ATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
genomic: GTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
EST: gi|5895663|gb|AW036909.1|AW036909
EST:     CCCTGCTGCTGAAGCAAAT                         ATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
genomic: CCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
EST: gi|113702008|gb|EE679512.1|EE679512
EST:     GCTTTCTTTGCGGCTGGAAATGTCAACCTTGCTGCTGAAGCAAAT                         ATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
genomic: GCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGAT
EST: gi|71439185|gb|DR820235.1|DR820235
EST:     TGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTNGA-GCAAAT                         ATCCATGGAGACCC
genomic: TGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCT-GAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCC

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), 49 (downstream exon)
Score: 54

CAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTACTGGGTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGATATCGTTGTGGTTGGCATTAACATAACAACACAAGTCTGCCTGACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 144

CAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTACTGGGTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGATATCGTTGTGGTTGGCATTAACATAACAACACAAGTCTGCCTGACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 118

CAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTACTGGGTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGATATCGTTGTGGTTGGCATTAACATAACAACACAAGTCTGCCTGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 382

CAAAAGAGACCCTTCCTTTGCAAGCAAGGTTAAGAAAATAGTTGTACTGGGTGGAGCTTTCTTTGCGGCTGGAAATGTCAACCCTGCTGCTGAAGCAAATgtatgataac ... tacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGATATCGTTGTGGTTGGCATTAACATAACAACACAAGTCTGCCTGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaggaggctaatactttaacataagtattgaaccttgagtgcattacactgcagATCCATGGAGACCCAGAAGCAGCTGACATAGTTTTTACTTCAGGAGCAGATATCGTTGTGGTTGGCATTAACATAACAACACAAGTCTGCCTGACAG
              ctttaac  putative branch site (score: 382)
         taatactttaacataa  TA-rich tract