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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgggccttaactttagtcgtgcttattttagggcattctgagtttactcttttttttttgccatgttcttttgtgctctaacctgttcctaacactgcttgcagGTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGATGAGCTATCAGTACAAACAAACTAAAGTGCCATGGCAGTAGGTCTGGTC

Basic information

species Zea mays
transcript GRMZM2G100246_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100246_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g44900.2 (Oryza sativa), 3'ss of exon 14
--------------------------------------------------------------gtatgtgggccttaactttagtcgtgcttattttag-ggcattctgagtttactcttttttttttgccatgttcttttgtgctctaacctgttcctaacactgcttgcagGTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGATGAGCTATCAGTACAAACAAACTAAAGTGCCATGGCAGTAGGTCTGGTC
                                                                   | |   |     ||||  | ||| | | | |  | | |   | |    |||    |  |  || | |||   |||| | |||| || |  || |  |||||||||||| || ||||||||||| |||||||||||||||||||||| ||| ||||||||||| |||||||| ||||| || || |||| |  | |||| ||  ||
gtatgtttaataacatcattgcatgcatattagaatctattttctggcatggtattgctgtttccaatcgagttctctattagctgggctcagtatggcagtagtaatactaatttctaagatggtacccttcttcgactgtgtt-taacttgcttataccgttgcttgcagGTGTCAGAGAATCAAGAACGACTTCACATTTGAGTACAACTTCCTTGAGGATGAGCTGTCAGTACAGACAAATTAGAGAGCCAGGATATTAGGGCTAATC
















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|37381481|gb|CF627630.1|CF627630
EST:     GGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATG                         GTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGA
genomic: GGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATGgtatgtgggc ... ctgcttgcagGTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGA
EST: gi|8665864|gb|BE186680.1|BE186680
EST:     GGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATG                         GTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGA
genomic: GGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATGgtatgtgggc ... ctgcttgcagGTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGA
EST: gi|60357172|gb|DN224145.1|DN224145
EST:     GGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATG                         GTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGA
genomic: GGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATGgtatgtgggc ... ctgcttgcagGTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGA
EST: gi|74238444|gb|DT646358.1|DT646358
EST:     GGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATG                         GTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGA
genomic: GGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATGgtatgtgggc ... ctgcttgcagGTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGA
EST: gi|74238445|gb|DT646359.1|DT646359
EST:     GGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATG                         GTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGA
genomic: GGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATGgtatgtgggc ... ctgcttgcagGTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGA
EST: gi|60342982|gb|DN209955.1|DN209955
EST:     GGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATG                         GTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGA
genomic: GGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATGgtatgtgggc ... ctgcttgcagGTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGA
EST: gi|30087988|gb|CB886193.1|CB886193
EST:     GGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATG                         GTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGA
genomic: GGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATGgtatgtgggc ... ctgcttgcagGTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGA

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), 48 (downstream exon)
Score: 111

GGTTCCAGCGGCATGTGGAGCCACAGGTCACGACTGATGAGTATGAGCGGGGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATGgtatgtgggc ... ctgcttgcagGTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGATGAGCTATCAGTACAAACAAACTAAAGTGCCATGGCAGTAGGTCTGGTC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 30

GGTTCCAGCGGCATGTGGAGCCACAGGTCACGACTGATGAGTATGAGCGGGGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATGgtatgtgggc ... ctgcttgcagGTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGATGAGCTATCAGTACAAACAAACTAAAGTGCCATGGCAGTAGGTCTGGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

GGTTCCAGCGGCATGTGGAGCCACAGGTCACGACTGATGAGTATGAGCGGGGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATGgtatgtgggc ... ctgcttgcagGTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGATGAGCTATCAGTACAAACAAACTAAAGTGCCATGGCAGTAGGTCTGGTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 104

GGTTCCAGCGGCATGTGGAGCCACAGGTCACGACTGATGAGTATGAGCGGGGATCATATGTATACTTTGATTTCCATGTCACTGAGGATGGCTCAGGATGgtatgtgggc ... ctgcttgcagGTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGATGAGCTATCAGTACAAACAAACTAAAGTGCCATGGCAGTAGGTCTGGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttttgccatgttcttttgtgctctaacctgttcctaacactgcttgcagGTGCCAAAGAATCAAGAATGACTTCACATTTGAGTACAACTACCTGGAGGATGAGCTATCAGTACAAACAAACTAAAGTGCCATGGCAGTAGGTCTGGTC
                                     tcctaac  putative branch site (score: 104)
                ttctttt  TA-rich tract