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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaattcccacaatttgtttctgcagagttgcttttcctgagattaaccaatactccctatcatctagacttctgttttatttcacgtttctttaacagctattattttttcgtgtaatcaacgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG

Basic information

species Zea mays
transcript GRMZM2G033619_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 17
gtaagtaattcccacaatttgtttctgcaga---gttgcttttcctg-agattaaccaatactccctatcatctagacttctgttttatt-tcacgtttctttaacagctattattttttcgtgtaatcaacgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG
|||||||||   | || | | ||| | |||    |  ||||  | |  | ||     |  |    | ||| | |  | | ||   ||||| | | |||| |||  ||  | | |||         | |  |  ||   |||||| || |||||||||||||||||||| || |||||||||||||||||||| ||| ||||||| |||
gtaagtaatgatctcagtatttttgtacagttacgcagcttggcttatatatggtgtagaaacatcaatcttgttcattgcttccttattataatgtttatttttca--tttcattgaagatctcatttcaatttttgcagGTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG
















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|22491346|gb|BU051269.1|BU051269
EST:     TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCA                         GTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
genomic: TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCAgtaagtaatt ... cgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
EST: gi|16925300|gb|BM078368.1|BM078368
EST:     GTCCATGAACAGCTGTGTGTGATGCTTGAGCA                         GTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
genomic: GTCCATGAACAGCTGTGTGTGATGCTTGAGCAgtaagtaatt ... cgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
EST: gi|19351428|gb|BM895945.1|BM895945
EST:     TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCA                         GTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
genomic: TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCAgtaagtaatt ... cgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
EST: gi|87156943|gb|DY401732.1|DY401732
EST:     TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCA                         GTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
genomic: TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCAgtaagtaatt ... cgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
EST: gi|87151915|gb|DY396704.1|DY396704
EST:     TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCA                         GTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
genomic: TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCAgtaagtaatt ... cgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
EST: gi|14203062|gb|BG836739.1|BG836739
EST:     TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCA                         GTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTMTCTTCCAAAGATTGT
genomic: TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCAgtaagtaatt ... cgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
EST: gi|60401098|gb|DN233905.1|DN233905
EST:     TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCA                         GTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
genomic: TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCAgtaagtaatt ... cgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
EST: gi|211177497|gb|FL246406.1|FL246406
EST:     TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCA                         GTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGK
genomic: TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCAgtaagtaatt ... cgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
EST: gi|149038585|gb|EE155512.2|EE155512
EST:     TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCA                         GTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT
genomic: TTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCAgtaagtaatt ... cgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGT

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: 43 (upstream exon), 46 (downstream exon)
Score: 74

GTAATTCCTGCCTGGTTAAGTTGCCTTCCGATAAAAAATGATTTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCAgtaagtaatt ... cgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 62

GTAATTCCTGCCTGGTTAAGTTGCCTTCCGATAAAAAATGATTTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCAgtaagtaatt ... cgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 79

GTAATTCCTGCCTGGTTAAGTTGCCTTCCGATAAAAAATGATTTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCAgtaagtaatt ... cgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 57

GTAATTCCTGCCTGGTTAAGTTGCCTTCCGATAAAAAATGATTTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCAgtaagtaatt ... cgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttcacgtttctttaacagctattattttttcgtgtaatcaacgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG
             ctttaac  putative branch site (score: 57)
                    agctattatttttt  TA-rich tract