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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatactctgtatgtccacattctaaagggcttggtcattgcgatgccaaatacttatattttgctagatggcaagctaatttactgaactttttttgttcccatcttgagaaggtatttctaattatatggccttctggtgcttttgctaaattttctctcattttttgccatcctattgtttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGA

Basic information

species Zea mays
transcript GRMZM2G435373_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G435373_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 3'ss of exon 9
gtgaatactctgta-tgtccacattctaaagggcttggtcattgcgatgccaaatacttatatt---ttgctagatggcaagctaatttactgaactttttttgttcccatcttgagaaggtatttctaattatatggccttctggtgcttttgctaaattttctctcattttttgccatcctattgtttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGA
|| |||  ||| |  |||   || | ||     |      |||    | |   ||  | || |    || |||||||     ||    | || |||   ||     |  || |        |  ||||     |       |   |   ||||  ||| |     | |||||  ||   |       ||| | |||||||||||||||| || | |||||  || ||||||||||| ||||||||||||||  | |  |||||||| || ||||| || || ||||||||||| ||||
gttaattttctttcctgtattcaatttatttaccacatgaattttctttcagtatgttcatttaggattcctagatgatgtacttccat-cttaacacattcacagcaaatttactattttttcttcttcccttccatttgttgagaagttttattaactacaaccacatttgatgttctgtatacatttattaacagGTTAGGAAGATAGGGAAAGTTGCACGAGCAATTGCTATAATGAGCCACCCAATTGCAAGCACAAATGACTCTCACTCAGTCCAGATTATTTTGCCACAGA

upper sequence: GRMZM2G435373_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 3'ss of exon 9
gtgaatactctgtatgtccacattctaaagggcttggtcattgcgatgccaaatacttatattttgctagatggcaagctaatttactgaactttttttgttcccatcttgagaaggtatttctaattatatggccttctggtgcttttgctaaattttctctcattttttgccatcctattgtttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGA
|| |||  ||| |    |   ||||   |  |  | ||  ||   ||      | ||   || ||  || ||| ||   |   |  |   |  ||     ||    |          |  ||||     |       |       ||||  ||| |     |||||||  ||   | ||   |||| | |||||||||||||||| || | |||||  || || |||||||| ||||||||||| ||  | || |||||||| || ||||| || || ||||||||||| ||||
gttaattttcttt---cctgtattcagcacaggattgttcttttaatatgttcttctgggatatt--taaatgtcatattccatctcaagatattcacaattgaacttactgtgtttttcttctgcccttccatttgttgataagttttattaactgcaacctcatttgatgttctgcttacgtttattaacagGTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCGATTGCAAACACAAATGACTCGCACTCAGTCCAGATTATTTTGCCACAGA
















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|6031345|gb|AW076202.1|AW076202
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAAT
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAAT
EST: gi|24934285|gb|CA452503.1|CA452503
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|67031426|gb|CO460175.1|CO460175
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|33095264|gb|CF055258.1|CF055258
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|32856054|gb|CD995735.1|CD995735
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|47962286|gb|CN844995.1|CN844995
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|33102234|gb|CF062194.1|CF062194
EST:     AAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: AAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|211034436|gb|FL381555.1|FL381555
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|211445979|gb|FL406296.1|FL406296
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|211259815|gb|FL426651.1|FL426651
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|32919393|gb|CF024205.1|CF024205
EST:     GCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: GCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
EST: gi|211346475|gb|FL413228.1|FL413228
EST:     CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAG                         GTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA
genomic: CTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCA

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: 488

TGAATTCGATATGGAGGGGAAAGTGTGTGGTGTCACATCTGAAGGTGAAACTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 513

TGAATTCGATATGGAGGGGAAAGTGTGTGGTGTCACATCTGAAGGTGAAACTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 336

TGAATTCGATATGGAGGGGAAAGTGTGTGGTGTCACATCTGAAGGTGAAACTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

TGAATTCGATATGGAGGGGAAAGTGTGTGGTGTCACATCTGAAGGTGAAACTGCAAAGTGCAAGAAGGTGGTCTGTGATCCTTCGTATTTACCAAACAAGgtgaatactc ... ttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgcttttgctaaattttctctcattttttgccatcctattgtttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGA
         tgctaaa  putative branch site (score: 327)
                                         ttgtttct  putative PPT
      ttttgctaaatttt  TA-rich tract