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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatcttgtttggcaacaatcttcttccctttatcctctttgtcgcttaattggattactacattaaaacctgacacaagcattccctcaacaacaacaacaacaacaacaaactgacacaagttatggatggcattgcagGTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGTACAATGGCGGGAGAGTTTGCACACAGGAACGTGCCCCCAGCCGTCGGTTG

Basic information

species Zea mays
transcript GRMZM2G108228_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108228_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g59130.1 (Oryza sativa), 3'ss of exon 4
gtgaatcttgtttggcaacaatcttcttccctttatcctctttgtcgcttaattggattactacattaaaacctgacacaagcattccctcaacaacaacaacaacaacaacaaactgacacaagttatggatggcattgcagGTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGTACAATGGCGGGAGAGTTTGCACACAGGAACGTGCCCCCAGCCGTCGGTTG---
                               |  |    ||||| |  | |||    ||  | ||   | |  || ||||  ||     |||    ||   |||   | || || |||||| |    ||||     ||||||||||||||||||| || || ||||| |||||||| ||||| ||| |||| |||||||   ||| | ||||| |||| |||||  |    |||||||||||    
------------------------------gtaaagttcctttgcca-tcaatc---ttcttgcacccacat-tgtcacatacacgtggtca----cagatacatgcataataatctgacatacaccatgg----tattgcagGTCAAATTTCCTCGGCACCAAATTCATCATCTATGACACGCAGCCTCCATACAATGCTCGGACACTTTGCTCACAAGAACGGACG---AGCCGTCGGTTCTCC
















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|32942208|gb|CF047027.1|CF047027
EST:     GACTCGAGGAATTTCTCCCGATCGAGCACTGGCTACATTGGGAAGCTAAG                         GTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGTA
genomic: GACTCGAGGAATTTCTCCCGATCGAGCACTGGCTACATTGGGAAGCTAAGgtgaatcttg ... ggcattgcagGTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGTA
EST: gi|30087730|gb|CB885936.1|CB885936
EST:     GACTCGAGGAATTTCTCCCGATCGAGCACTGGCTACATTGGGAAGCTAAG                         GTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGTA
genomic: GACTCGAGGAATTTCTCCCGATCGAGCACTGGCTACATTGGGAAGCTAAGgtgaatcttg ... ggcattgcagGTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGTA
EST: gi|32843854|gb|CD983535.1|CD983535
EST:     GACTCGAGGAATTTCTCCCGATCGAGCACTGGCTACATTGGGAAGCTAAG                         GTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGT
genomic: GACTCGAGGAATTTCTCCCGATCGAGCACTGGCTACATTGGGAAGCTAAGgtgaatcttg ... ggcattgcagGTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGT
EST: gi|78111744|gb|DV530141.1|DV530141
EST:     GACTCGAGGAATTTCTCCCGATCGAGCACTGGCTACATTGGGAAGCTAAG                         GTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGTA
genomic: GACTCGAGGAATTTCTCCCGATCGAGCACTGGCTACATTGGGAAGCTAAGgtgaatcttg ... ggcattgcagGTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGTA
EST: gi|32844683|gb|CD984364.1|CD984364
EST:     GACTCGAGGAATTTCTCCCGATCGAGCACTGGCTACATTGGGAAGCTAAG                         GTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGT
genomic: GACTCGAGGAATTTCTCCCGATCGAGCACTGGCTACATTGGGAAGCTAAGgtgaatcttg ... ggcattgcagGTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGT

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: 73

CAGCGAAAAGGAGCCGCAGGATGGCGCACACGGAGTATGCAATTTTTATGGACTCGAGGAATTTCTCCCGATCGAGCACTGGCTACATTGGGAAGCTAAGgtgaatcttg ... ggcattgcagGTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGTACAATGGCGGGAGAGTTTGCACACAGGAACGTGCCCCCAGCCGTCGGTTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 102

CAGCGAAAAGGAGCCGCAGGATGGCGCACACGGAGTATGCAATTTTTATGGACTCGAGGAATTTCTCCCGATCGAGCACTGGCTACATTGGGAAGCTAAGgtgaatcttg ... ggcattgcagGTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGTACAATGGCGGGAGAGTTTGCACACAGGAACGTGCCCCCAGCCGTCGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

CAGCGAAAAGGAGCCGCAGGATGGCGCACACGGAGTATGCAATTTTTATGGACTCGAGGAATTTCTCCCGATCGAGCACTGGCTACATTGGGAAGCTAAGgtgaatcttg ... ggcattgcagGTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGTACAATGGCGGGAGAGTTTGCACACAGGAACGTGCCCCCAGCCGTCGGTTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 144

CAGCGAAAAGGAGCCGCAGGATGGCGCACACGGAGTATGCAATTTTTATGGACTCGAGGAATTTCTCCCGATCGAGCACTGGCTACATTGGGAAGCTAAGgtgaatcttg ... ggcattgcagGTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGTACAATGGCGGGAGAGTTTGCACACAGGAACGTGCCCCCAGCCGTCGGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcaacaacaacaacaacaacaacaaactgacacaagttatggatggcattgcagGTCAAATTTCCTTGGAACTAAATTTATCATCTACGACACACAGGCTCCGTACAATGGCGGGAGAGTTTGCACACAGGAACGTGCCCCCAGCCGTCGGTTG
                         aactgac  putative branch site (score: 144)
                                  aagttat  TA-rich tract