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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGTGTGGTGGATAGCAGCCGAATTTTGAGAGAAATTGCTTCTCCTCAACTGAATGAGTTTGCGGATAAAATCCATCTTGATGCCCAAGATAGCCCAAGgtttgttcgtatgccatgccatgttttggaactgaaatttgattccgcaaaatcctgacgaatactgaagcacttgtagcctcgtttattgaggggcctgtgcatgatctaattggaagtttctgttaacag

Basic information

species Zea mays
transcript GRMZM2G098828_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098828_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os09g21510.1 (Oryza sativa), 5'ss of exon 15
GCAGTGTGGTGGATAGCAGCCGAATTTTGAGAGAAATTGCTTCTCCTCAACTGAATGAGTTTGCGGATAAAATCCATCTTGATGCCCAAGATAGCCCAAGgtttgt-tcgtat--------gccatgccatgttttggaactgaaatttgattccgcaaaatcctgacgaatactgaagc----acttgtagcctcgtt-tattgaggggcctgtgcatgatctaattggaagtttctgttaacag------------------------------------
        ||  | ||||||||||||||||||||||| |||||||| |||||  ||||||| |   | |||||||||  ||||| ||||||||||||||||||||| ||  ||          ||   |||||| || ||   ||  |   | ||  |  |   |    || || |   |    | |  | ||    || || ||| | | |   |  |  |  | |||    | |   |||||                                      
AAGACACTGTACAGAGCAGCCGAATTTTGAGAGAAATAGCTTCTCCGCAACTTGATGAGTTAGGAAACAAAATCCATTCTGATGTCCAAGATAGCCCAAGgtttgtgtcaaattgctttgaaacacagcatgttatgcaaaaaaagctaactgccttactaatgtag-aaacaccgggtctgggattcattgcaatattctagtgatgtggccaagtgtcttgca-ttgattatctgctttaaccatcaacaatctaattgctggaccatttctgttaacag
















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|31363668|gb|CD448025.1|CD448025
EST:     CTGAATGAGTTTGCGGATAAAATCCATCTTGATGCCCAAGATAGCCCAAG                         CATCAGCTTCACCGAAAGGCAGAGGAAGTGGAAAGAAGAGTTGGACCAGGA
genomic: CTGAATGAGTTTGCGGATAAAATCCATCTTGATGCCCAAGATAGCCCAAGgtttgttcgt ... ctgttaacagCATCAGCTTCACCGAAAGGCAGAGGAAGTGGAAAGAAGAGTTGGACCAGGA
EST: gi|60344956|gb|DN211929.1|DN211929
EST:     CCAAGATAGCCCAAG                         CATCAGCTTCACCGAAAGGCAGAGGAAGTGGAAAGAAGAGTTGGACCAGGA
genomic: CCAAGATAGCCCAAGgtttgttcgt ... ctgttaacagCATCAGCTTCACCGAAAGGCAGAGGAAGTGGAAAGAAGAGTTGGACCAGGA
EST: gi|78106821|gb|DV525239.1|DV525239
EST:     TAAAATCCATCTTGATGCCCAAGATAGCCCAAG                         CATCAGCTTCACCGAAAGGCAGAGGAAGTGGAAAGAAGAGTTGGACCAGGA
genomic: TAAAATCCATCTTGATGCCCAAGATAGCCCAAGgtttgttcgt ... ctgttaacagCATCAGCTTCACCGAAAGGCAGAGGAAGTGGAAAGAAGAGTTGGACCAGGA

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), 42 (downstream exon)
Score: 77

GCAGTGTGGTGGATAGCAGCCGAATTTTGAGAGAAATTGCTTCTCCTCAACTGAATGAGTTTGCGGATAAAATCCATCTTGATGCCCAAGATAGCCCAAGgtttgttcgt ... ctgttaacagCATCAGCTTCACCGAAAGGCAGAGGAAGTGGAAAGAAGAGTTGGACCAGGAACTTGAGAGGGAGAGAG


Block sizes: 47 (upstream exon), 31 (downstream exon)
Score: 14

GCAGTGTGGTGGATAGCAGCCGAATTTTGAGAGAAATTGCTTCTCCTCAACTGAATGAGTTTGCGGATAAAATCCATCTTGATGCCCAAGATAGCCCAAGgtttgttcgt ... ctgttaacagCATCAGCTTCACCGAAAGGCAGAGGAAGTGGAAAGAAGAGTTGGACCAGGAACTTGAGAGGGAGAGAG


Block sizes: 48 (upstream exon), 30 (downstream exon)
Score: 6

GCAGTGTGGTGGATAGCAGCCGAATTTTGAGAGAAATTGCTTCTCCTCAACTGAATGAGTTTGCGGATAAAATCCATCTTGATGCCCAAGATAGCCCAAGgtttgttcgt ... ctgttaacagCATCAGCTTCACCGAAAGGCAGAGGAAGTGGAAAGAAGAGTTGGACCAGGAACTTGAGAGGGAGAGAG


Block sizes: 48 (upstream exon), 32 (downstream exon)
Score: 22

GCAGTGTGGTGGATAGCAGCCGAATTTTGAGAGAAATTGCTTCTCCTCAACTGAATGAGTTTGCGGATAAAATCCATCTTGATGCCCAAGATAGCCCAAGgtttgttcgt ... ctgttaacagCATCAGCTTCACCGAAAGGCAGAGGAAGTGGAAAGAAGAGTTGGACCAGGAACTTGAGAGGGAGAGAG