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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtctatttttatcttcagccactgtaatgggcatgaggcactggttgaaatggctctacctgtgttggttttacgggtgatgaaccttattttaatttggtcatgacatgccacagATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATTGATCCAACATACATGCTCCGCGCTGTGCGAGCCAATGCATCCGATGCCA

Basic information

species Zea mays
transcript GRMZM2G009591_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009591_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os10g26570.1 (Oryza sativa), 3'ss of exon 12
gttagtctatttttatcttcagccactgtaatgggcatgaggcactggttgaaatggctctacctgtgttg-gttttacgggtgatg----aaccttattttaatttggtcatgacatgccacagATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATTGATCCAACATACATGCTCCGCGCTGTGCGAGCCAATGCATCCGATGCCA
                                                | |||    ||  ||||   |   || | |    | |      || |  | | ||| ||   | || |||||||||||||||| ||||||| ||||| |||||||| ||||||||||| ||||| |||||||| ||||||||| |||| |||||||| |||||||||||||||||||
---------------------------------------gtttgtccatcgaatgaccttcaccttgatgatgtatcaaaaatcacatgccaaaccaaatctaacttaaccgtgccatgccacagATCAAGGCCCATTTCAAGGAAATAGGAGTACATTCTGATGTGAAGTACATTGATCCTACATACATGGTCCGTGCTGTGCGTGCCAATGCATCCGATGCCA
















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|92088053|gb|EB484284.1|EB484284
EST:     CATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAG                         ATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGGATATT
genomic: CATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAGgttagtctat ... catgccacagATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATT
EST: gi|78119430|gb|DV537814.1|DV537814
EST:     CATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAG                         ATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATT
genomic: CATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAGgttagtctat ... catgccacagATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATT
EST: gi|67014533|gb|CO443282.1|CO443282
EST:     CATCANGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAG                         ATCAAGTCCCATTNTAAGGACATANGAGTNCATTCTGATGTCAAGTATATT
genomic: CATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAGgttagtctat ... catgccacagATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATT
EST: gi|160481643|gb|EY254213.1|EY254213
EST:     CATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAG                         ATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATT
genomic: CATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAGgttagtctat ... catgccacagATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATT
EST: gi|5713662|gb|AI943654.1|AI943654
EST:     CATCAGGGAACATGGTTNTTAGTGCCATTGGTGTGCCCCTTCAGCAGAAG                         ATCAAGTCCCATTTTAAGGCCATAGGAGTCCATTTTGATGTCAAGTATATT
genomic: CATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAGgttagtctat ... catgccacagATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATT
EST: gi|91056415|gb|EB166833.1|EB166833
EST:     CATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAG                         ATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATT
genomic: CATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAGgttagtctat ... catgccacagATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATT
EST: gi|94477845|gb|EB706803.1|EB706803
EST:     CATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAG                         ATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATT
genomic: CATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAGgttagtctat ... catgccacagATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATT

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), 45 (downstream exon)
Score: 24

GAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAGgttagtctat ... catgccacagATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATTGATCCAACATACATGCTCCGCGCTGTGCGAGCCAATGCATCCGATGCCA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 73

GAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAGgttagtctat ... catgccacagATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATTGATCCAACATACATGCTCCGCGCTGTGCGAGCCAATGCATCCGATGCCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 106

GAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAGgttagtctat ... catgccacagATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATTGATCCAACATACATGCTCCGCGCTGTGCGAGCCAATGCATCCGATGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

GAATACTTTCAAAAGTCAAATGCAACTGATGCATCAGGGAACATGGTTCTTAGTGACATTGGTGTGCACCTTCAGCAGAAGgttagtctat ... catgccacagATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATTGATCCAACATACATGCTCCGCGCTGTGCGAGCCAATGCATCCGATGCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttggttttacgggtgatgaaccttattttaatttggtcatgacatgccacagATCAAGTCCCATTTTAAGGACATAGGAGTCCATTCTGATGTCAAGTATATTGATCCAACATACATGCTCCGCGCTGTGCGAGCCAATGCATCCGATGCCA
                            ttttaat  putative branch site (score: 109)
                     aaccttattttaattt  TA-rich tract