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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccccttgttttgtttcaggatggcattactgtagtgttgtatttcatatttgttgctttgaagttttaatatcttatgagtgaacggcttggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA

Basic information

species Zea mays
transcript GRMZM2G170291_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170291_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g18200.1 (Oryza sativa), 3'ss of exon 6
ccccttgttttgtttcaggatggcattactgtagtgttgtatttcatatttgttgctttgaagttt--taatatcttatgagtgaacggcttggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA
  |  || || | |  |||||  | ||| |  | ||    |   |||| || | |  ||||| |||  ||||| || |||    ||    ||| |  |||||||||||||||||||||||||||||  | ||||||||||| |||||||| ||  ||||||| |||||||| || ||||||||||||||
--caatgcttggatctaggatccccttagttcattgcaacaagacatacttctaggcttgaaattttttaatacctcatggagtaattatttgaatttacagAGGAAAGCTGGTAGATGCTTACAGATATCTGCACAAAGAGAAGGACATGGATTGTGGCTTTTCTTGGTCTGGACATCCAATTGGCAA

upper sequence: GRMZM2G170291_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv17s0000g09970.t01 (Vitis vinifera), 3'ss of exon 6
-ccccttgttttgtttcaggatggcatta-ctgtagtgttgtatttca-tatttgttgctttgaagttttaatatcttatgagtgaacggcttggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA
 ||     ||   ||      |  ||||   | ||   || || | || | ||  |   |||||  | ||| |   ||  ||||    || ||   | | ||| || ||||| |||||||| ||||| | ||| ||||| ||||| ||||| || ||||||||||| ||||| ||  | || ||||| ||
gcctgaacttcaattcttacctttcattggttatacctttataatgcagtgttaatgaatttgagctcttactggttt--gagtctgtggattatgc-ttcagGGGGAAGCTAGTAGATGCATACAGACTCCTACACAAGGAAAAAGACATGGAAGGTGGCTTCTCATGGTCTGGAAACCCTATTGGAAA
















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|18167261|gb|BM337100.1|BM337100
EST:     TTTGGCAACATATTATTCCA                         AGGGAAGCTGGTAAATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: TTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|91872354|gb|EB402311.1|EB402311
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|5030707|gb|AI714901.1|AI714901
EST:     CCCAGCAGA-AGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|91873536|gb|EB403493.1|EB403493
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|93284180|gb|EB676444.1|EB676444
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|74236587|gb|DT644501.1|DT644501
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|76016190|gb|DT943360.1|DT943360
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|50332549|gb|CO527675.1|CO527675
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|6465582|gb|AW191177.1|AW191177
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|76021195|gb|DT948365.1|DT948365
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|78024045|gb|DV492432.1|DV492432
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|86472832|gb|DY239202.1|DY239202
EST:     CCAGCAGAGAGGCGGCGTTTTGGCAACATATTTTTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCCCAAAGAAAAGGACATAGA
genomic: CCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|211321948|gb|FK966254.1|FK966254
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|89757610|gb|DY687139.1|DY687139
EST:     AGAGACGGCGTTTTGGCAACATATTATTTCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: AGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|76014034|gb|DT941204.1|DT941204
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|149043280|gb|EE047341.2|EE047341
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|76018499|gb|DT945669.1|DT945669
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|78105399|gb|DV523817.1|DV523817
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|60351954|gb|DN218927.1|DN218927
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|60356095|gb|DN223068.1|DN223068
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|76014035|gb|DT941205.1|DT941205
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|18661354|gb|BM501369.1|BM501369
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
EST: gi|71771441|gb|DR969378.1|DR969378
EST:     CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCA                         AGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA
genomic: CCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGA

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

GACTGTGGACAGCCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 20

GACTGTGGACAGCCAGGATTCACCCCAGCAGAGAGACGGCGTTTTGGCAACATATTATTCCAgtaggtgaaa ... ggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttgttgctttgaagttttaatatcttatgagtgaacggcttggacatacagAGGAAAGCTGGTAGATGCTTACAGGCACCTGCACAAAGAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA
                  ttttaat  putative branch site (score: 20)
           tttgaagttttaatat  TA-rich tract