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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtataccaccattatgtatgagttcatatttgtttcttctatgctactacacgtggtttttcgtctggagcattgatggctttgcttctgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAGGGGTATACTTTGGCTGGGCAGGACTTTCAACGCGTGGTATATATAAGAT

Basic information

species Zea mays
transcript GRMZM2G027115_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027115_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g14814.1 (Oryza sativa), 3'ss of exon 7
tagtataccaccattatgtatgagttcatatttgtttcttctatgctactacacgtggtttttcgtctggag-----cattgatggctttgcttctgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAGGGGTATACTTTGGCTGGGCAGGACTTTCAACGCGTGGTATATATAAGAT
      ||||     | |||      |  |||  ||| ||| || |||  |  |    |||    | ||        || |||| ||| |   | |    | |||| || ||||| || || || |||||||||||| | ||||| ||||||||| ||||||||||||||||||| |||||||||||||| ||||||||||||||
----ggaccatgtcaaagtactcaaccg-attaattttttcaatactagcatgcccaatttccattgtgagcactgtcactgatagctatatattttccttgcagCCAACTTACCTGCAGAAAACTTTTCCGACGTACTATCAGAGCATACATCAAGGGTATACTTTGGCTGGGCTGGACTTTCAACGCGAGGTATATATAAGAT

upper sequence: GRMZM2G027115_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g32730.1 (Oryza sativa), 3'ss of exon 8
--tagtataccaccattatgtatgagttcatatttgtttcttctatgctactacacgtggtttttcgtctggagcattgatggctttgcttctgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAGGGGTATACTTTGGCTGGGCAGGACTTTCAACGCGTGGTATATATAAGAT
  |  |  ||||     | |||      |  |||  ||| ||| ||||||  |  |  |  ||| | |   ||||| |||| ||| |   | |    | |||| || ||||| || || || || ||||||||| | ||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||| ||||||
tttgctggaccatgtcaaagtactcagccg-attcattttttcaatgctagcatgc-cgaatttccattgtgagcactgatagctatatattttccttgcagCCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAGGGGTATACTTTGGCTGGGCTGGACTTTCAACGCGAGGTATATTTAAGAT
















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|19822013|gb|BQ048037.1|BQ048037
EST:     TGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAG                         CAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
genomic: TGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAGgtatgacttg ... tgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
EST: gi|32921306|gb|CF026118.1|CF026118
EST:     ACTAGGAATACCAACAG                         CAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
genomic: ACTAGGAATACCAACAGgtatgacttg ... tgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
EST: gi|211114268|gb|FL244779.1|FL244779
EST:     GATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAG                         CAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
genomic: GATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAGgtatgacttg ... tgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
EST: gi|76018985|gb|DT946155.1|DT946155
EST:     TGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAG                         CAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
genomic: TGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAGgtatgacttg ... tgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
EST: gi|18169104|gb|BM338944.1|BM338944
EST:     TGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAG                         CAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
genomic: TGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAGgtatgacttg ... tgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
EST: gi|15499363|gb|BI595876.1|BI595876
EST:     TGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAG                         CAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
genomic: TGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAGgtatgacttg ... tgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
EST: gi|166457337|gb|EG142685.1|EG142685
EST:     TGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAG                         CTAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCA
genomic: TGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAGgtatgacttg ... tgtactacagC-AAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCA
EST: gi|18169085|gb|BM338925.1|BM338925
EST:     TGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAG                         CAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
genomic: TGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAGgtatgacttg ... tgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
EST: gi|71447208|gb|DR828258.1|DR828258
EST:     TGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAG                         CAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG
genomic: TGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAGgtatgacttg ... tgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAG

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), 49 (downstream exon)
Score: 42

GGATTGAAGGTACCTTACCAATAGAACCATGGTTTATTGGTGGGCCTGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAGgtatgacttg ... tgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAGGGGTATACTTTGGCTGGGCAGGACTTTCAACGCGTGGTATATATAAGAT


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

GGATTGAAGGTACCTTACCAATAGAACCATGGTTTATTGGTGGGCCTGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAGgtatgacttg ... tgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAGGGGTATACTTTGGCTGGGCAGGACTTTCAACGCGTGGTATATATAAGAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 48

GGATTGAAGGTACCTTACCAATAGAACCATGGTTTATTGGTGGGCCTGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAGgtatgacttg ... tgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAGGGGTATACTTTGGCTGGGCAGGACTTTCAACGCGTGGTATATATAAGAT


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

GGATTGAAGGTACCTTACCAATAGAACCATGGTTTATTGGTGGGCCTGTGATCAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATACCAACAGgtatgacttg ... tgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAGGGGTATACTTTGGCTGGGCAGGACTTTCAACGCGTGGTATATATAAGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactacacgtggtttttcgtctggagcattgatggctttgcttctgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAGGGGTATACTTTGGCTGGGCAGGACTTTCAACGCGTGGTATATATAAGAT
                           cattgat  putative branch site (score: 49)
                                    ctttgcttct  putative PPT
             ttttt  TA-rich tract