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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgccgagaaacgaactcattccgatttactttttcttggagaattaactattagaatgttttctttctttggtagGATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACAACCTTCCTGAGACG

Basic information

species Zea mays
transcript GRMZM2G305254_T06
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G305254_T07 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 5
gtttgtgccgagaaacgaactc--------attccgatttactttttct----tggagaattaac-----tattagaatgttttc-----tttcttt---ggtagGATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACAACCTTCCTGAGACG
|| ||||   ||||| | | |          |||| |||||||||||||    | || |  | ||     | || | ||  |||      |||||||   || ||||||||||||||||| |||||||| || || || || |||||||||||||||||||||
gtctgtgtgcagaaatggaatgtgaagaagtttcccatttactttttctatgatagaaaggttacattgttgttggtatcattttattcatttcttttgtggcagGATATTTGCTTTGGCAACTGTCTTGAGTTCAGTGCTAATCTACAACCTTCCTGAGACG
















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|148930272|gb|EC872750.2|EC872750
EST:     GACACTGAAGGGTTTGAAAGTGTTGGGAAATCAAATGTGTATGATGATAG                         GATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACA
genomic: GACACTGAAGGGTTTGAAAGTGTTGGGAAATCAAATGTGTATGATGATAGgtttgtgccg ... tctttggtagGATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACA
EST: gi|148936664|gb|EC880790.2|EC880790
EST:     GACACTGAAGGGTTTGAAAGTGTTGGGAAATCAAATGTGTATGATGATAG                         GATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACAACCTTCC
genomic: GACACTGAAGGGTTTGAAAGTGTTGGGAAATCAAATGTGTATGATGATAGgtttgtgccg ... tctttggtagGATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACAACCTTCC
EST: gi|160481497|gb|EY254329.1|EY254329
EST:     GACACTGAAGGGTTTGAAAGTGTTGGGAAATCAAATGTGTATGATGATAG                         GATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACAACCTTCC
genomic: GACACTGAAGGGTTTGAAAGTGTTGGGAAATCAAATGTGTATGATGATAGgtttgtgccg ... tctttggtagGATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACAACCTTCC
EST: gi|149107780|gb|EE292141.2|EE292141
EST:     GACACTGAAGGGTTTGAAAGTGTTGGGAAATCAAATGTGTATGATGATAG                         GATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACAACCTTCC
genomic: GACACTGAAGGGTTTGAAAGTGTTGGGAAATCAAATGTGTATGATGATAGgtttgtgccg ... tctttggtagGATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACAACCTTCC

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: 47

CTCCTGTTGAGATGGATGTTGATGGTTCCAAAGTTTCTGTCCTTTATCTAGACACTGAAGGGTTTGAAAGTGTTGGGAAATCAAATGTGTATGATGATAGgtttgtgccg ... tctttggtagGATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACAACCTTCCTGAGACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 40

CTCCTGTTGAGATGGATGTTGATGGTTCCAAAGTTTCTGTCCTTTATCTAGACACTGAAGGGTTTGAAAGTGTTGGGAAATCAAATGTGTATGATGATAGgtttgtgccg ... tctttggtagGATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACAACCTTCCTGAGACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 44

CTCCTGTTGAGATGGATGTTGATGGTTCCAAAGTTTCTGTCCTTTATCTAGACACTGAAGGGTTTGAAAGTGTTGGGAAATCAAATGTGTATGATGATAGgtttgtgccg ... tctttggtagGATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACAACCTTCCTGAGACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 49

CTCCTGTTGAGATGGATGTTGATGGTTCCAAAGTTTCTGTCCTTTATCTAGACACTGAAGGGTTTGAAAGTGTTGGGAAATCAAATGTGTATGATGATAGgtttgtgccg ... tctttggtagGATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACAACCTTCCTGAGACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgatttactttttcttggagaattaactattagaatgttttctttctttggtagGATATTTGCTTTGGCGACTGTCTTAAGCTCGGTCCTTATCTACAACCTTCCTGAGACG
                     aattaac  putative branch site (score: 49)
                                    tgttttctttcttt  putative PPT
                     aattaactattagaat  TA-rich tract