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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaacaacaaaggattctctatgaaactacatgcatttacgagccttgtgtactagccaagtgacaagtgtttttttaatgtattttgttttatgtcagGGATTACCTACTAAGTATACGGGGACTGGGGCTTAAAAGTGTTGAATGTGTTCGTCTTCTCACACTGCATCATCTTGCTTTCCCT

Basic information

species Zea mays
transcript GRMZM2G131756_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131756_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g37410.1 (Oryza sativa), 3'ss of exon 8
taaaacaacaaaggattctctatgaaactacatgcatttacgagccttgtgtactagccaagtgacaagtgttt---ttttaatgtattttgttttatgtcagGGATTACCTACTAAGTATACGGGGACTGGGGCTTAAAAGTGTTGAATGTGTTCGTCTTCTCACACTGCATCATCTTGCTTTCCCT
  || ||   ||||||| | | |   |    |    | |   |  | | | || ||  || |||| |||| | |   ||  ||||| ||    ||  | |||||||||| || || |||||||| ||| ||||||| ||||||||||| || || || ||| | ||| | ||||||||||| ||||| 
--aagcagtcaaggattttttttaggaaagaaaat-tctgtcaatcctatttattacacaggtgagaagtatgtcgattacaatgtgttcgaattattttcagGGATTATCTGCTTAGTATACGCGGATTGGGGCTCAAAAGTGTTGAGTGCGTCCGCCTTTTGACATTACATCATCTTGCATTCCCA

upper sequence: GRMZM2G131756_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g37350.1 (Oryza sativa), 3'ss of exon 7
taaaacaacaaagga-ttctctatgaaactacatgcatttacgagccttgtgtactagccaagtgacaagtgttt---ttttaatgtattttgttttatgtcagGGATTACCTACTAAGTATACGGGGACTGGGGCTTAAAAGTGTTGAATGTGTTCGTCTTCTCACACTGCATCATCTTGCTTTCCCT
     ||   ||||| || | | | |    | |    |  | || || | | || |   || | || |||| | |   ||  ||||| ||    ||  | ||||||| || || || |||||||| ||| ||||||| ||||||||||| ||||| || ||| | ||| | ||||||||||| ||||| 
----gcagtgaaggaatttttttttaggaaagaaaattccatgaaccctatttatttcacaggcgagaagtatgtcaattacaatgtgttcgaattattttcagGGACTATCTGCTTAGTATACGTGGATTGGGGCTCAAAAGTGTTGAGTGTGTCCGCCTTTTGACATTACATCATCTTGCATTCCCA
















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|22546703|gb|BU099014.1|BU099014
EST:     GGGAGCATTGACCTTGAGTGGCTAAGATATATTCCCCCAGACTCAGCGAA                         GGATTACCTACTAAGTATACGGGGACTGGGGCTTAAAAGTGTTGAATGTGT
genomic: GGGAGCATTGACCTTGAGTGGCTAAGATATATTCCCCCAGACTCAGCGAAgtaagatcct ... tttatgtcagGGATTACCTACTAAGTATACGGGGACTGGGGCTTAAAAGTGTTGAATGTGT
EST: gi|87156096|gb|DY400885.1|DY400885
EST:     GGGAGCATTGACCTTGAGTGGCTAAGATATATTCCCCCAGACTCAGCGAA                         GGATTACCTACTAAGTATACGGGGACTGGGGCTTAAAAGTGTTGAATGTGT
genomic: GGGAGCATTGACCTTGAGTGGCTAAGATATATTCCCCCAGACTCAGCGAAgtaagatcct ... tttatgtcagGGATTACCTACTAAGTATACGGGGACTGGGGCTTAAAAGTGTTGAATGTGT
EST: gi|26559363|gb|CA831598.1|CA831598
EST:     TAAGATATATTCCCCCAGACTCAGCGAA                         GGATTACCTACTAAGTATACGGGGACTGGGGCTTAAAAGTGTTGAATGTGT
genomic: TAAGATATATTCCCCCAGACTCAGCGAAgtaagatcct ... tttatgtcagGGATTACCTACTAAGTATACGGGGACTGGGGCTTAAAAGTGTTGAATGTGT

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: 48 (upstream exon), 49 (downstream exon)
Score: 253

AATTTTCTGAATCGTTTGGTTAGAGATCATGGGAGCATTGACCTTGAGTGGCTAAGATATATTCCCCCAGACTCAGCGAAgtaagatcct ... tttatgtcagGGATTACCTACTAAGTATACGGGGACTGGGGCTTAAAAGTGTTGAATGTGTTCGTCTTCTCACACTGCATCATCTTGCTTTCCCT


Block sizes: 37 (upstream exon), 47 (downstream exon)
Score: 22

AATTTTCTGAATCGTTTGGTTAGAGATCATGGGAGCATTGACCTTGAGTGGCTAAGATATATTCCCCCAGACTCAGCGAAgtaagatcct ... tttatgtcagGGATTACCTACTAAGTATACGGGGACTGGGGCTTAAAAGTGTTGAATGTGTTCGTCTTCTCACACTGCATCATCTTGCTTTCCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 63

AATTTTCTGAATCGTTTGGTTAGAGATCATGGGAGCATTGACCTTGAGTGGCTAAGATATATTCCCCCAGACTCAGCGAAgtaagatcct ... tttatgtcagGGATTACCTACTAAGTATACGGGGACTGGGGCTTAAAAGTGTTGAATGTGTTCGTCTTCTCACACTGCATCATCTTGCTTTCCCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 49

AATTTTCTGAATCGTTTGGTTAGAGATCATGGGAGCATTGACCTTGAGTGGCTAAGATATATTCCCCCAGACTCAGCGAAgtaagatcct ... tttatgtcagGGATTACCTACTAAGTATACGGGGACTGGGGCTTAAAAGTGTTGAATGTGTTCGTCTTCTCACACTGCATCATCTTGCTTTCCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtgtactagccaagtgacaagtgtttttttaatgtattttgttttatgtcagGGATTACCTACTAAGTATACGGGGACTGGGGCTTAAAAGTGTTGAATGTGTTCGTCTTCTCACACTGCATCATCTTGCTTTCCCT
                             ttttaat  putative branch site (score: 49)
                                       ttttgtttt  putative PPT
                     aagtgtttttttaatg  TA-rich tract