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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttaaaggtcatatgagatatttgagtggtcctggtattctatcaataactcctatgtttctgcctgtggttattgacaattttctcatacgatacagCTGCAACACATGGGAATATGTCGTTCAGCTTGATTTCTGCAGCTGATGCTCTATTGGGTTCATCTGCAACCAAGTACAGTGCATTAGATTGCCAGAGGCC

Basic information

species Zea mays
transcript GRMZM2G114394_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114394_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 6
actttaaaggtcatatgagatatttgagtggtcctggtattctatcaataactcctatgtttctgcctgtggtta-ttgacaattttctcatacga-tacagCTGCAACACATGGGAATATGTCGTTCAGCTTGATTTCTGCAGCTGATGCTCTATTGGGTTCATCTGCAACCAAGTACAGTGCATTAGATTGCCAGAGGCC
  ||   || |   |    || |   |    | | || | |||  || | ||    |  ||||| | |||||||| || ||| |||||||||  |  |||||||||||| |||| |||||  || |||||| |||||||||| |||||||||||  ||||||||||||| |||||||||||||||||||||||||| |||||
tgttactagattgca-atcatgtc-aacaaatgcaggcaatctgacagttacatagaaatttctacttgtggttaatttacagttttctcatttggctacagCTGCAACCCATGAGAATAAATCATTCAGCCTGATTTCTGCGGCTGATGCTCTGCTGGGTTCATCTGCCACCAAGTACAGTGCATTAGATTGCCAAAGGCC
















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|31351455|gb|CD435812.1|CD435812
EST:     TCATTTAACACTAGGAAATGGAAAACTTCTCTCTGGGCTTGGAGTATCAC                         CTGCAACACATGGGAATATGTCATTCAGCTTGATTTCTGCAGCTGATGCTC
genomic: TCATTTAACACTAGGAAATGGAAAACTTCTCTCTGGGCTTGGAGTATCACgtaagtattt ... tacgatacagCTGCAACACATGGGAATATGTCGTTCAGCTTGATTTCTGCAGCTGATGCTC
EST: gi|31354263|gb|CD438620.1|CD438620
EST:     TCATTTAACACTAGGAAATGGAAAACTTCTCTCTGGGCTTGGAGTATCAC                         CTGCAACACATGGGAATATGTCATTCAGCTTGATTTCTGCAGCTGATGCTC
genomic: TCATTTAACACTAGGAAATGGAAAACTTCTCTCTGGGCTTGGAGTATCACgtaagtattt ... tacgatacagCTGCAACACATGGGAATATGTCGTTCAGCTTGATTTCTGCAGCTGATGCTC
EST: gi|28909947|gb|CB331179.1|CB331179
EST:     TCATTTAACACTAGGAAATGGAAAACTTCTCTCTGGGCTTGGAGTATCAC                         CTGCAACACATGGGAATATGTCGTTCAGCTTGATTTCTGCAGCTGATGCTC
genomic: TCATTTAACACTAGGAAATGGAAAACTTCTCTCTGGGCTTGGAGTATCACgtaagtattt ... tacgatacagCTGCAACACATGGGAATATGTCGTTCAGCTTGATTTCTGCAGCTGATGCTC
EST: gi|67043292|gb|CO469547.1|CO469547
EST:     TCATTTAACACTAGGAAATGGAAAACTTCTCTCTGGGCTTGGAGTATCAC                         CTGCAACACATGGGAATATGTCATTCAGCTTGATTTCTGCAGCTGATGCTC
genomic: TCATTTAACACTAGGAAATGGAAAACTTCTCTCTGGGCTTGGAGTATCACgtaagtattt ... tacgatacagCTGCAACACATGGGAATATGTCGTTCAGCTTGATTTCTGCAGCTGATGCTC

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: 49 (upstream exon), 49 (downstream exon)
Score: 214

CCATGGATAACTACTGTTGCTGCTGGAGTTGATGACCGCAGATACAAGAATCATTTAACACTAGGAAATGGAAAACTTCTCTCTGGGCTTGGAGTATCACgtaagtattt ... tacgatacagCTGCAACACATGGGAATATGTCGTTCAGCTTGATTTCTGCAGCTGATGCTCTATTGGGTTCATCTGCAACCAAGTACAGTGCATTAGATTGCCAGAGGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 41

CCATGGATAACTACTGTTGCTGCTGGAGTTGATGACCGCAGATACAAGAATCATTTAACACTAGGAAATGGAAAACTTCTCTCTGGGCTTGGAGTATCACgtaagtattt ... tacgatacagCTGCAACACATGGGAATATGTCGTTCAGCTTGATTTCTGCAGCTGATGCTCTATTGGGTTCATCTGCAACCAAGTACAGTGCATTAGATTGCCAGAGGCC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 10

CCATGGATAACTACTGTTGCTGCTGGAGTTGATGACCGCAGATACAAGAATCATTTAACACTAGGAAATGGAAAACTTCTCTCTGGGCTTGGAGTATCACgtaagtattt ... tacgatacagCTGCAACACATGGGAATATGTCGTTCAGCTTGATTTCTGCAGCTGATGCTCTATTGGGTTCATCTGCAACCAAGTACAGTGCATTAGATTGCCAGAGGCC


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

CCATGGATAACTACTGTTGCTGCTGGAGTTGATGACCGCAGATACAAGAATCATTTAACACTAGGAAATGGAAAACTTCTCTCTGGGCTTGGAGTATCACgtaagtattt ... tacgatacagCTGCAACACATGGGAATATGTCGTTCAGCTTGATTTCTGCAGCTGATGCTCTATTGGGTTCATCTGCAACCAAGTACAGTGCATTAGATTGCCAGAGGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caataactcctatgtttctgcctgtggttattgacaattttctcatacgatacagCTGCAACACATGGGAATATGTCGTTCAGCTTGATTTCTGCAGCTGATGCTCTATTGGGTTCATCTGCAACCAAGTACAGTGCATTAGATTGCCAGAGGCC
                            tattgac  putative branch site (score: 49)
                                     ttttctcat  putative PPT
                           ttattgacaatttt  TA-rich tract