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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgccctgcataatctacgtcctgtccactataacatttcagttcagaaatattatcttatcatgatgatttattattttcatagGTTCTCGAACAATTGGTGTTATCACAAAG

Basic information

species Zea mays
transcript GRMZM2G129155_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129155_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 2
gtatgtgtgccctgcataatctacgtcctgtccactataacatttcagttcagaaatatta--tcttatcatga--tgatttattattttcatagGTTCTCGAACAATTGGTGTTATCACAAAG
            |    | |  |    |  |||| || |  |||   ||| | | || ||   |||||| |  |  ||||| ||| || |  ||||||||||||||||||||||||| ||||||
-----------gtattcactacagactcaatccattagataattcatgttaatatattttgtttcttattaataattgattcattgttcttgtagGTTCTCGAACAATTGGTGTTATAACAAAG
















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|149075510|gb|EE164038.2|EE164038
EST:     TTTAGCAAACTCTGATGCTCTTCAAATGGCTCGGGTTGCTGATCCTGATG                         GTTCTCGAACAATTGGTGTTATCACAAAG
genomic: TTTAGCAAACTCTGATGCTCTTCAAATGGCTCGGGTTGCTGATCCTGATGgtatgtgtgc ... attttcatagGTTCTCGAACAATTGGTGTTATCACAAAG
EST: gi|91874421|gb|EB404378.1|EB404378
EST:     TTTAGCAAACTCTGATGCTCTTCAAATGGCTCGGGTTGCTGATCCTGATG                         GTTCTCGAACAATTGGTGTTATCACAAAG
genomic: TTTAGCAAACTCTGATGCTCTTCAAATGGCTCGGGTTGCTGATCCTGATGgtatgtgtgc ... attttcatagGTTCTCGAACAATTGGTGTTATCACAAAG
EST: gi|91874420|gb|EB404377.1|EB404377
EST:     TTTAGCAAACTCTGATGCTCTTCAAATGGCTCGGGTTGCTGATCCTGATG                         GTTCTCCGAACA-TTGGTGTTATCACAAAGTTGG
genomic: TTTAGCAAACTCTGATGCTCTTCAAATGGCTCGGGTTGCTGATCCTGATGgtatgtgtgc ... attttcatagGTTCTC-GAACAATTGGTGTTATCACAAAGTTGG

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: 46 (upstream exon), 35 (downstream exon)
Score: 161

ATCAGGCACAAGACATGCATCATCTTAGCTGTTTCGCCAGCAAATGCAGATTTAGCAAACTCTGATGCTCTTCAAATGGCTCGGGTTGCTGATCCTGATGgtatgtgtgc ... attttcatagGTTCTCGAACAATTGGTGTTATCACAAAG


Block sizes: 46 (upstream exon), 36 (downstream exon)
Score: 184

ATCAGGCACAAGACATGCATCATCTTAGCTGTTTCGCCAGCAAATGCAGATTTAGCAAACTCTGATGCTCTTCAAATGGCTCGGGTTGCTGATCCTGATGgtatgtgtgc ... attttcatagGTTCTCGAACAATTGGTGTTATCACAAAG


Block sizes: 48 (upstream exon), 29 (downstream exon)
Score: 169

ATCAGGCACAAGACATGCATCATCTTAGCTGTTTCGCCAGCAAATGCAGATTTAGCAAACTCTGATGCTCTTCAAATGGCTCGGGTTGCTGATCCTGATGgtatgtgtgc ... attttcatagGTTCTCGAACAATTGGTGTTATCACAAAG


Block sizes: 46 (upstream exon), 29 (downstream exon)
Score: 195

ATCAGGCACAAGACATGCATCATCTTAGCTGTTTCGCCAGCAAATGCAGATTTAGCAAACTCTGATGCTCTTCAAATGGCTCGGGTTGCTGATCCTGATGgtatgtgtgc ... attttcatagGTTCTCGAACAATTGGTGTTATCACAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataacatttcagttcagaaatattatcttatcatgatgatttattattttcatagGTTCTCGAACAATTGGTGTTATCACAAAG
 ctataac  putative branch site (score: 195)
                                           ttattttc  putative PPT
                 aaatattatcttatca  TA-rich tract