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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgctaaactttctacctgtttttttcctgctctattgagctttgatgccaatggttgttgtacagGCAGCTTGCAATATACACTGGTCCAACAG

Basic information

species Zea mays
transcript GRMZM2G040017_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 3
gtaagctgctaaactttctacctgtttttttcctgctctattgagctttgatgccaatggttgttgtacagGCAGCTTGCAATATACACTGGTCCAACAG
|| || |  | |||| |  |||| ||||||||   |  ||||  | ||| |    ||    |||| ||||||||||| ||||||||||||||||||||||
gtgagttagtgaactctagacctatttttttctgaccttatttcg-tttaacctaaactactgttctacagGCAGCTCGCAATATACACTGGTCCAACAG
















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|71769706|gb|DR967643.1|DR967643
EST:     AGCATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGA                         GCAGCTTGCAATATACACTGGTCCAACAG
genomic: AGCATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGAgtaagctgct ... tgttgtacagGCAGCTTGCAATATACACTGGTCCAACAG
EST: gi|149075133|gb|EE163627.2|EE163627
EST:     AGCATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGA                         GCAGCTTGCAATATACACTGGTCCAACAG
genomic: AGCATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGAgtaagctgct ... tgttgtacagGCAGCTTGCAATATACACTGGTCCAACAG
EST: gi|149072532|gb|EE160814.2|EE160814
EST:     AGCATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGA                         GCAGCTTGCAATATACACTGGTTCAACAG
genomic: AGCATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGAgtaagctgct ... tgttgtacagGCAGCTTGCAATATACACTGGTCCAACAG
EST: gi|89760510|gb|DY688889.1|DY688889
EST:     AGCATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGA                         GCAGCTTGCAATATACACTGGTCCAACAG
genomic: AGCATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGAgtaagctgct ... tgttgtacagGCAGCTTGCAATATACACTGGTCCAACAG
EST: gi|60339318|gb|DN206291.1|DN206291
EST:     CATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGA                         GCAGCTTGCAATATACACTGGTCCAACAG
genomic: CATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGAgtaagctgct ... tgttgtacagGCAGCTTGCAATATACACTGGTCCAACAG
EST: gi|149085154|gb|EE174658.2|EE174658
EST:     AGCATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGA                         GCAGCTTGCAATATACACTGGTCCAACAG
genomic: AGCATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGAgtaagctgct ... tgttgtacagGCAGCTTGCAATATACACTGGTCCAACAG

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), 29 (downstream exon)
Score: 60

GGATTGATTTTCCTTTTCAGCATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGAgtaagctgct ... tgttgtacagGCAGCTTGCAATATACACTGGTCCAACAG


Block sizes: 49 (upstream exon), 29 (downstream exon)
Score: 105

GGATTGATTTTCCTTTTCAGCATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGAgtaagctgct ... tgttgtacagGCAGCTTGCAATATACACTGGTCCAACAG


Block sizes: 49 (upstream exon), 29 (downstream exon)
Score: 112

GGATTGATTTTCCTTTTCAGCATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGAgtaagctgct ... tgttgtacagGCAGCTTGCAATATACACTGGTCCAACAG


Block sizes: 49 (upstream exon), 29 (downstream exon)
Score: 176

GGATTGATTTTCCTTTTCAGCATGCTAGGAATAACACCTTTAGCTGAGCGTTTAGGATATGCAACTGAgtaagctgct ... tgttgtacagGCAGCTTGCAATATACACTGGTCCAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctacctgtttttttcctgctctattgagctttgatgccaatggttgttgtacagGCAGCTTGCAATATACACTGGTCCAACAG
                             ctttgat  putative branch site (score: 176)
      tgttttttt  TA-rich tract