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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggtgcttacttttgaggccctagtccgtccctgtcagccttgtaagtgtagtttcagacattggtacagtcagtctgtctaacatcttgtgaattgaagTGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGCCGTGCCAC

Basic information

species Zea mays
transcript GRMZM2G051004_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 2
gtaagtggtgcttacttttgaggccctagtccgtccctgtcagccttgtaagtgtagtttcagacattggtacagtc--agtctgtctaa--catcttgtgaattgaagTGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGCCGTGCCAC
|||| ||   | | ||| | | ||| || | | |||   ||    ||||||| |   |||       || |   ||   |     |||||   || || | || | |||||| ||| |||| |||||| |||||||||||||||| ||||| ||||||||||| ||||
gtaactg---cctgcttctaatgcc-tatttcttcctcttcg---ttgtaagagcgcttttttgatctgattatgttttaacgcatctaaataatttttttaactcaagTGCTAGGAACATTGAGCCGCTGAGAGCGATAGCTACTCAGGCACCCCCTGCCGTCCCAC
















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|149005302|gb|EE039851.2|EE039851
EST:     TCAGCCCATTTCGGCCGCGCCTTCCCCTCCGTCGCGGTCTCCTCTTTGGC                         TGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGC
genomic: TCAGCCCATTTCGGCCGCGCCTTCCCCTCCGTCGCGGTCTCCTCTTTGGCgtaagtggtg ... tgaattgaagTGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGC
EST: gi|31612121|gb|CD568743.1|CD568743
EST:     TCAGCCCATTTCGGCCGCGCCTTCCCCTCCGTCGCGGTCTCCTCTTTGGC                         TGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGC
genomic: TCAGCCCATTTCGGCCGCGCCTTCCCCTCCGTCGCGGTCTCCTCTTTGGCgtaagtggtg ... tgaattgaagTGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGC
EST: gi|31664252|gb|CD572977.1|CD572977
EST:     TCAGCCCATTTCGGCCGCGCCTTCCCCTCCGTCGCGGTCTCCTCTTTGGC                         TGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGC
genomic: TCAGCCCATTTCGGCCGCGCCTTCCCCTCCGTCGCGGTCTCCTCTTTGGCgtaagtggtg ... tgaattgaagTGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGC
EST: gi|29946974|gb|CB816419.1|CB816419
EST:     TCAGCCCATTTCGG-CGCG-CTTCCCCTCCGTCGCGG-CTCCTCTTTGGC                         TGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGC
genomic: TCAGCCCATTTCGGCCGCGCCTTCCCCTCCGTCGCGGTCTCCTCTTTGGCgtaagtggtg ... tgaattgaagTGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGC

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), 49 (downstream exon)
Score: 141

GTTCCGTGCGTGAGGAGCACTGGTTCAGCCCATTTCGGCCGCGCCTTCCCCTCCGTCGCGGTCTCCTCTTTGGCgtaagtggtg ... tgaattgaagTGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGCCGTGCCAC


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 74

GTTCCGTGCGTGAGGAGCACTGGTTCAGCCCATTTCGGCCGCGCCTTCCCCTCCGTCGCGGTCTCCTCTTTGGCgtaagtggtg ... tgaattgaagTGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGCCGTGCCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

GTTCCGTGCGTGAGGAGCACTGGTTCAGCCCATTTCGGCCGCGCCTTCCCCTCCGTCGCGGTCTCCTCTTTGGCgtaagtggtg ... tgaattgaagTGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGCCGTGCCAC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 187

GTTCCGTGCGTGAGGAGCACTGGTTCAGCCCATTTCGGCCGCGCCTTCCCCTCCGTCGCGGTCTCCTCTTTGGCgtaagtggtg ... tgaattgaagTGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGCCGTGCCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtagtttcagacattggtacagtcagtctgtctaacatcttgtgaattgaagTGCGAGGCACATCGAGCCGATGAGAGCGATAGCTACACAGGCGCCCCCTGCCGTGCCAC
                                gtctaac  putative branch site (score: 187)
                                               aattgaa  TA-rich tract