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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtactgtacacatgatcagttgaacggcctgtacatgatcagatggattcgcgccttaacgctcatccggtccggtgctctggcgtgtgcagATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG

Basic information

species Zea mays
transcript GRMZM2G095126_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095126_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os10g35070.2 (Oryza sativa), 3'ss of exon 9
------------------gtctgtactgtacacatgatcagttgaa-cggcctgtacatgatcagatggattcgcgccttaacgctcatccggtccggtgctctggcgtgtg-cagATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG
                       || |      || ||||||| || |    | |  ||  ||| |||      |   ||       |    | |   |  | ||  || || |||| ||||||||||||||||| ||||| || || |||||||||  ||||||| |||| || |||||||||||||| |||||||||
gtcagtgaatcactgacgaatcatattac-tgtatcatcagttcaatccatgtctgaatt-tcaaatg---ctacagtttcgtctaaacttaggcatataatttgtggtttgtcagACCCGGACATGCTGGAGGTTGGCAATGGCGGGATGACCAACGACGAGTACATCGTCCATTTCAGCCTCTGGGCCATCTCCAAG

upper sequence: GRMZM2G095126_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os10g35070.4 (Oryza sativa), 3'ss of exon 10
------------------gtctgtactgtacacatgatcagttgaa-cggcctgtacatgatcagatggattcgcgccttaacgctcatccggtccggtgctctggcgtgtg-cagATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG-----------------
                       || |      || ||||||| || |    | |  ||  ||| |||      |   ||       |    | |   |  | ||  || || |||| ||||||||||||||||| ||||| || || |||||||||  ||||||| |||| || |||||||||||||| |||||||||                 
gtcagtgaatcactgacgaatcatattac-tgtatcatcagttcaatccatgtctgaatt-tcaaatg---ctacagtttcgtctaaacttaggcatataatttgtggtttgtcagACCCGGACATGCTGGAGGTTGGCAATGGCGGGATGACCAACGACGAGTACATCGTCCATTTCAGCCTCTGGGCCATCTCCAAGGTACTACCAAATGTGAC
















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|71323535|gb|DR798428.1|DR798428
EST:     GCGCGCCCCGGCGGATGGAACG                         ATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACG
genomic: GCGCGCCCCGGCGGATGGAACGgtctgtactg ... gcgtgtgcagATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACG
EST: gi|88753305|gb|DY537446.1|DY537446
EST:     CCAGAACGAGGTGTGGTGGGAGTACGCGCGCCCCGGCGGATGGAACG                         ATCCGGACATGCTGGAGGGGGGCAACGGGGGCAGGCCCAACAGCGAGTACG
genomic: CCAGAACGAGGTGTGGTCGGAGTACGCGCGCCCCGGCGGATGGAACGgtctgtactg ... gcgtgtgcagATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACG
EST: gi|149080680|gb|EE169738.2|EE169738
EST:     GGACCAGAACGAGGTGTGGTCGGAGTACGCGCGCCCCGGCGGATGGAACG                         ATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACG
genomic: GGACCAGAACGAGGTGTGGTCGGAGTACGCGCGCCCCGGCGGATGGAACGgtctgtactg ... gcgtgtgcagATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACG
EST: gi|71767715|gb|DR965652.1|DR965652
EST:     GGACCAGAACGAGGTGTGGTCGGAGTACGCGCGCCCCGGCGGATGGAACG                         ATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACG
genomic: GGACCAGAACGAGGTGTGGTCGGAGTACGCGCGCCCCGGCGGATGGAACGgtctgtactg ... gcgtgtgcagATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACG

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), 15 (downstream exon)
Score: 5

CATGATCGCCACGGCGGACCAGAACGAGGTGTGGTCGGAGTACGCGCGCCCCGGCGGATGGAACGgtctgtactg ... gcgtgtgcagATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG


Block sizes: 47 (upstream exon), 35 (downstream exon)
Score: 33

CATGATCGCCACGGCGGACCAGAACGAGGTGTGGTCGGAGTACGCGCGCCCCGGCGGATGGAACGgtctgtactg ... gcgtgtgcagATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 78

CATGATCGCCACGGCGGACCAGAACGAGGTGTGGTCGGAGTACGCGCGCCCCGGCGGATGGAACGgtctgtactg ... gcgtgtgcagATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 9

CATGATCGCCACGGCGGACCAGAACGAGGTGTGGTCGGAGTACGCGCGCCCCGGCGGATGGAACGgtctgtactg ... gcgtgtgcagATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcagatggattcgcgccttaacgctcatccggtccggtgctctggcgtgtgcagATCCGGACATGCTGGAGGTGGGCAACGGGGGCATGACCAACAGCGAGTACGTCGTGCACTTCAGCCTCTGGGCGATCTCCAAG
                ccttaac  putative branch site (score: 9)