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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaatactatttctctttctacctgtttccatgtagcattcattagtgcttctgcaattaataggcatcaagtgcttatgtaggactcagATGAATTGAGAAAAGATGGCGCTGAAGAAATTTTGGAAGATATTACTGACCTTGTCAATGAAACCATCTTTGATGATGGTTCATATAACATTTCGTTTAC

Basic information

species Zea mays
transcript GRMZM2G152757_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152757_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g08280.1 (Oryza sativa), 3'ss of exon 3
gtaacaata--ctatttctctttctacct----gtttccatgtagcattcattagtgcttctgcaattaataggcatcaagtgcttatgtaggactcagATGAATTGAGAAAAGATGGCGCTGAAGAAATTTTGGAAGATATTACTGACCTTGTCAATGAAACCATCTTTGATGATGGTTCATATAACATTTCGTTTAC
||||  ||   || ||||| ||||| |||    ||||| ||| |     ||  ||| |||   ||||| || || || | || || ||||||||||| || |||||||| ||||| ||||| ||||||||||| ||| |||| || || || || || ||||| ||| | ||||||||| |||| | |||||       
gtaattatcatctgtttctgtttctgcctactggtttcgatggacagcgcacaagt-ctttcacaattgattgggat-atgtactcatgtagGACTCGGAAGAATTGAGGAAAGAAGGCGCAGAAGAAATTTTAGAAAATATCACCGAGCTCGTAAACGAAACTATCGTAGATGATGGTACATACAGCATTT-------
















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|211140497|gb|FL400397.1|FL400397
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|211140497|gb|FL400397.1|FL400397
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|50326445|gb|CO521571.1|CO521571
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|50326445|gb|CO521571.1|CO521571
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|211426998|gb|FL426768.1|FL426768
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|211426998|gb|FL426768.1|FL426768
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|71435796|gb|DR816846.1|DR816846
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|71435796|gb|DR816846.1|DR816846
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|93012264|gb|EB637784.1|EB637784
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|93012264|gb|EB637784.1|EB637784
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|15208795|gb|BI430679.1|BI430679
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|15208795|gb|BI430679.1|BI430679
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|211027069|gb|FL381517.1|FL381517
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|211027069|gb|FL381517.1|FL381517
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|211217102|gb|FL383485.1|FL383485
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|211217102|gb|FL383485.1|FL383485
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|211084814|gb|FL392700.1|FL392700
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|211084814|gb|FL392700.1|FL392700
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|211131362|gb|FL428332.1|FL428332
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|211131362|gb|FL428332.1|FL428332
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|91048113|gb|EB158531.1|EB158531
EST:     CCTTNAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|91048113|gb|EB158531.1|EB158531
EST:     CCTTNAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|149037768|gb|EE155430.2|EE155430
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|149037768|gb|EE155430.2|EE155430
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|211225357|gb|FL370946.1|FL370946
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-
EST: gi|211225357|gb|FL370946.1|FL370946
EST:     CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAG                         G
genomic: CCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcag-

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 1 RNA-Seqlibrary.


Block sizes: 16 (upstream exon), 48 (downstream exon)
Score: 5

GATCTCAAATATTGGTCGGTTTTTCCTTAAAGATGGATGTATCATCTGGACCATTTTCATTGGTGGCTGAAGAGgtaacaatac ... taggactcagATGAATTGAGAAAAGATGGCGCTGAAGAAATTTTGGAAGATATTACTGACCTTGTCAATGAAACCATCTTTGATGATGGTTCATATAACATTTCGTTTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattcattagtgcttctgcaattaataggcatcaagtgcttatgtaggactcagATGAATTGAGAAAAGATGGCGCTGAAGAAATTTTGGAAGATATTACTGACCTTGTCAATGAAACCATCTTTGATGATGGTTCATATAACATTTCGTTTAC
                    aattaat  putative branch site (score: 5)
                    aattaata  TA-rich tract