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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattgatgatgctcttatgctagaatgttcttccaaattccctatgtatccttttatcttgatctgcaggaaattacactccttataaaccacataaattttcttcatgggaatttatgtgatcatactgtaatagtttactaataaagtaatacaaattgcagGTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG

Basic information

species Zea mays
transcript GRMZM2G080044_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080044_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g11140.1 (Oryza sativa), 3'ss of exon 3
gtaaattgatgatgctcttatgctagaatgttcttccaaattccc-------tatgtatccttttat----cttgatctgca--ggaaattacactccttataaaccacataaattttc-----ttcatgggaatttatgtgatcat-actgtaatagtttactaataaagtaatac-aaattgcagGTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG
||||| |||| ||||||||||||| |||  | | |  | |||  |       |||   |  ||||||    ||||||    |  ||  ||     |  ||  ||       |  || ||      ||||| | | |      |  ||   ||| ||| |||||||| ||| | | |  |  || |||||  | ||||||||||||||||| | |||||||||||| ||||||||||| ||||| ||||||||||
gtaaaatgatcatgctcttatgctggaaattccatttagatttgcagagtgctatacctgtttttatatatcttgatacataacggtcatagtggtgtttgcaatttgacaattttatcagtgactcatgtgcactcgctaaacaattgatgtgatattttactaagaaaatgaaattacgtttcagGTCATGCTGGTTGATCAATCTGACAGATTTGTATTTAAGCCCATGTTGTATGAGCTCTTGTCAGGAG
















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|30306789|gb|CD001462.1|CD001462
EST:     CCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAG                         GTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTAC
genomic: CCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAGgtaaattgat ... caaattgcagGTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTAC
EST: gi|29543792|gb|CB604172.1|CB604172
EST:     CCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAG                         GTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTAC
genomic: CCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAGgtaaattgat ... caaattgcagGTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTAC
EST: gi|31998276|gb|CD662009.1|CD662009
EST:     CCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAG                         GTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTAC
genomic: CCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAGgtaaattgat ... caaattgcagGTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTAC
EST: gi|211318171|gb|FL216129.1|FL216129
EST:     CCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAG                         GTTCTTCTGGTTGATCAATCTGA
genomic: CCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAGgtaaattgat ... caaattgcagGTTCTTCTGGTTGATCAATCTGA
EST: gi|211318168|gb|FL216126.1|FL216126
EST:     CCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAG                         GTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTAC
genomic: CCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAGgtaaattgat ... caaattgcagGTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTAC

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: 39

AGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAGgtaaattgat ... caaattgcagGTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 20

AGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAGgtaaattgat ... caaattgcagGTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 7

AGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAGgtaaattgat ... caaattgcagGTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 13

AGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAGgtaaattgat ... caaattgcagGTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatttatgtgatcatactgtaatagtttactaataaagtaatacaaattgcagGTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG
                             tactaat  putative branch site (score: 13)
                     taatagtttactaata  TA-rich tract