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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaactaattgttgcaatttcacagaattctttgattttcttctaaatactgtggtactgaggtgtaaaacttgtctttacagGACATTAGGTACCTGATGGAGGATGTGCAAGTGATGAAACCGACAATATTCTGTGGTGTTCCTCGTGTTTATGATCGTATATATACAG

Basic information

species Zea mays
transcript GRMZM2G104847_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104847_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 10
gtacgaactaattgttgcaatttcacagaattctttgattttcttcta-aatactgtggtac-tgaggtgtaaaacttgtctttacagGACATTAGGTACCTGATGGAGGATGTGCAAGTGATGAAACCGACAATATTCTGTGGTGTTCCTCGTGTTTATGATCGTATATATACAG
||| || |       || |   | |   | |   | || | ||||||   |   | ||| |  |||     |  |||| ||||  |||||||||||||| || ||||||||||||||| |||||||||| ||  |||| |||||||| ||||||||||||||||||||||| ||||
gtatgagcagcacaatgaaggatgaataattctgtagactatcttctttgaccatctggcaggtgacacaaaccactt-tcttaccagGACATTAGGTATCTCATGGAGGATGTGCAAATGATGAAACCAACGGTATTTTGTGGTGTCCCTCGTGTTTATGATCGTATATACACAG
















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|67024206|gb|CO452955.1|CO452955
EST:     TTGAGAACTACTGTATTTCTAAAGGAGCCTCCATCGGATTCTGGCAAGGG                         GACATTAGGTACCTGATGGAGGATGTGCAAGTGATGAAACCGACAATATTC
genomic: TTGAGAACTACTGTATTTCTAAAGGAGCCTCCATCGGATTCTGGCAAGGGgtacgaacta ... gtctttacagGACATTAGGTACCTGATGGAGGATGTGCAAGTGATGAAACCGACAATATTC
EST: gi|67024157|gb|CO452906.1|CO452906
EST:     TTGAGAACTACTGTATTTCTAAAGGAGCCTCCATCGGATTCTGGCAAGGG                         GACATTAGGTACCTGATGGAGGATGTGCAAGTGATGAAACCGACAATATTC
genomic: TTGAGAACTACTGTATTTCTAAAGGAGCCTCCATCGGATTCTGGCAAGGGgtacgaacta ... gtctttacagGACATTAGGTACCTGATGGAGGATGTGCAAGTGATGAAACCGACAATATTC
EST: gi|211399266|gb|FL448654.1|FL448654
EST:     TTGAGAACTACTGTATTTCTAAAGGAGCCTCCATCGGATTCTGGCAAGGG                         GACATTAGGTACCTGATGGAGGATGTGCAAGTGATGAACCCGACAGTACTC
genomic: TTGAGAACTACTGTATTTCTAAAGGAGCCTCCATCGGATTCTGGCAAGGGgtacgaacta ... gtctttacagGACATTAGGTACCTGATGGAGGATGTGCAAGTGATGAAACCGACAATATTC

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 358

GGATTCCTACTTTTCCTACCTTCCATTAGCACATATATTTGATCAAGTAATTGAGAACTACTGTATTTCTAAAGGAGCCTCCATCGGATTCTGGCAAGGGgtacgaacta ... gtctttacagGACATTAGGTACCTGATGGAGGATGTGCAAGTGATGAAACCGACAATATTCTGTGGTGTTCCTCGTGTTTATGATCGTATATATACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

GGATTCCTACTTTTCCTACCTTCCATTAGCACATATATTTGATCAAGTAATTGAGAACTACTGTATTTCTAAAGGAGCCTCCATCGGATTCTGGCAAGGGgtacgaacta ... gtctttacagGACATTAGGTACCTGATGGAGGATGTGCAAGTGATGAAACCGACAATATTCTGTGGTGTTCCTCGTGTTTATGATCGTATATATACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 504

GGATTCCTACTTTTCCTACCTTCCATTAGCACATATATTTGATCAAGTAATTGAGAACTACTGTATTTCTAAAGGAGCCTCCATCGGATTCTGGCAAGGGgtacgaacta ... gtctttacagGACATTAGGTACCTGATGGAGGATGTGCAAGTGATGAAACCGACAATATTCTGTGGTGTTCCTCGTGTTTATGATCGTATATATACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgattttcttctaaatactgtggtactgaggtgtaaaacttgtctttacagGACATTAGGTACCTGATGGAGGATGTGCAAGTGATGAAACCGACAATATTCTGTGGTGTTCCTCGTGTTTATGATCGTATATATACAG
            ttctaaa  putative branch site (score: 504)
                                          cttgtcttt  putative PPT
      attttcttctaaata  TA-rich tract