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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattttactccccagcaagttcatttaatctcctactgtctatatttagtcctgagatgcctttatttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG

Basic information

species Zea mays
transcript GRMZM2G063151_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063151_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g16700.4 (Oryza sativa), 3'ss of exon 4
gtaagattttactccccagcaagttcatttaatctccta-ctgtctatattt---------agtcctgagatgcct---ttatttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG
||||| |||  | ||     || |   ||| || |  ||  | | |   |||         ||||      |||||   ||  | |||||||| |||||||| || |||||||| || ||||||||||||||  |||| |||||||| | ||| |||||||| ||||| |||
gtaag-tttggccccatgaaaaatgtttttgatattgtaattattttggttttatggccatagtctaagactgcctgtttttctccttgcagTAAAACTTAGGATCAAGTCTTTCAAGGTGCCTGAACTTCTAATTGAGATCCCAGAAACTGCGACTGTTGGTTCACTGAAG
















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|211462608|gb|FK992343.1|FK992343
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211457563|gb|FK992319.1|FK992319
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211462609|gb|FK992344.1|FK992344
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211462605|gb|FK992340.1|FK992340
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|13558490|gb|BG549846.1|BG549846
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211465137|gb|FK992354.1|FK992354
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211460083|gb|FK992329.1|FK992329
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211460082|gb|FK992328.1|FK992328
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211462610|gb|FK992345.1|FK992345
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211457565|gb|FK992321.1|FK992321
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211460080|gb|FK992326.1|FK992326
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211457566|gb|FK992322.1|FK992322
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211460085|gb|FK992331.1|FK992331
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211462604|gb|FK992339.1|FK992339
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211465138|gb|FK992355.1|FK992355
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211462606|gb|FK992341.1|FK992341
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211460077|gb|FK992323.1|FK992323
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211460090|gb|FK992336.1|FK992336
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211457564|gb|FK992320.1|FK992320
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|13249860|gb|BG360765.1|BG360765
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         CGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211457560|gb|FK992316.1|FK992316
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211462603|gb|FK992338.1|FK992338
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
EST: gi|211462614|gb|FK992349.1|FK992349
EST:     GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATG                         TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC
genomic: GACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCC

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: 44 (upstream exon), 49 (downstream exon)
Score: 45

CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

CAAACAAGGGGACTAATTCAATGCCATTCCAGAAATCTTGTGGGTCAAATGATTGCCATGgtaagatttt ... tttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttaatctcctactgtctatatttagtcctgagatgcctttatttcttgcagTGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG
  atttaat  putative branch site (score: 169)
                                     tgcctttatttctt  putative PPT
                  tctatattta  TA-rich tract