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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggtgctctctgtcttgcctgcgcgcgcggtgggtcggtctcctcttgctcagtcatccatgtatgattgattgatcgctgtccgtcgccgctgcagGTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGACTGCATCCGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGAC

Basic information

species Zea mays
transcript GRMZM2G141922_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141922_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g02130.1 (Oryza sativa), 3'ss of exon 5
gtagggtgctctctgtcttgcctgcgcgcgcggtgggt------cggtctcctctt--gctcagtca--tccatgt----atgattgattgat-cgctgtccgtcgccgctgcagGTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGACTGCATCCGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGAC
      ||||     |||||   ||   |    |   |       | ||  || ||  |||| ||    ||| ||     |    |||||  |  | ||    |    | ||||| ||||| || ||||||||||| ||| |||| ||||| ||||||||| |||| |||||| |||| ||||| |||||||| || ||||| ||||| ||||| 
--gtaatgctgctgatcttggtggcatcccaaattaatgtttggtgatcagctgttcagctctgttggttccttgctaccagtgctgattcgtgtggtggtgttgtttgatgcagCTTCCCTGGAAGCACGTCGCTTCATTTGGCTGCTCGTAGCGGGAACTTGGATTGCATCAGGAAGCTGCTTGCCTGGGGAGCTGATCGGCTCCAAAGGGAT
















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|89756253|gb|DY686344.1|DY686344
EST:     GTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGG                         GTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGA
genomic: GTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGGgtagggtgct ... gccgctgcagGTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGA
EST: gi|87153855|gb|DY398644.1|DY398644
EST:     GTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGG                         GTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGA
genomic: GTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGGgtagggtgct ... gccgctgcagGTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGA
EST: gi|71435966|gb|DR817016.1|DR817016
EST:     GTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGG                         GTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGA
genomic: GTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGGgtagggtgct ... gccgctgcagGTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGA
EST: gi|76284382|gb|DV023950.1|DV023950
EST:     GTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGG                         GTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGA
genomic: GTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGGgtagggtgct ... gccgctgcagGTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGA
EST: gi|91869237|gb|EB400304.1|EB400304
EST:     GTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGG                         GTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGA
genomic: GTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGGgtagggtgct ... gccgctgcagGTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGA
EST: gi|19057993|gb|BM736660.1|BM736660
EST:     GTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGG                         GTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGA
genomic: GTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGGgtagggtgct ... gccgctgcagGTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGA

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: 45 (upstream exon), 47 (downstream exon)
Score: 132

CCACGCCGCTGCACCTCGCCGCCAGGCAGGGCCGCTCCGCCTGCGTGCAGGTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGGgtagggtgct ... gccgctgcagGTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGACTGCATCCGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGAC


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 26

CCACGCCGCTGCACCTCGCCGCCAGGCAGGGCCGCTCCGCCTGCGTGCAGGTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGGgtagggtgct ... gccgctgcagGTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGACTGCATCCGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGAC


Block sizes: 42 (upstream exon), 46 (downstream exon)
Score: 26

CCACGCCGCTGCACCTCGCCGCCAGGCAGGGCCGCTCCGCCTGCGTGCAGGTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGGgtagggtgct ... gccgctgcagGTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGACTGCATCCGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGAC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 54

CCACGCCGCTGCACCTCGCCGCCAGGCAGGGCCGCTCCGCCTGCGTGCAGGTGCTGCTGGAGAACGGCGCCATTGTCTCCGCCCTCACCGGCTCCTACGGgtagggtgct ... gccgctgcagGTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGACTGCATCCGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttgctcagtcatccatgtatgattgattgatcgctgtccgtcgccgctgcagGTTCCCCGGCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGACTGCATCCGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGAC
                           gattgat  putative branch site (score: 54)
                    tatgatt  TA-rich tract