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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaggatcacctaacctaactctatgttgtagttccagccttctgggttatgtttgttggaactaacttctgtttcaatcactattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA

Basic information

species Zea mays
transcript GRMZM2G005493_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
gtatgaggatcacctaacctaactctatgttgtagttccagccttctgggtt---atgtttgttgga--actaacttctgtttcaatcactattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA
|||||   || ||||    | |   |  | |  |||||     || ||  ||   | ||||| |  |  |  ||||||||| | |||   ||||||||||||||||||||||||||||||||||||||| || |||||||  |||||||||||||| |||||||||||||||||||| ||||| |||   
gtatggctattacctggtttcatgtttaggttcagttca----ttatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG

upper sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 6
gtatgaggatcacctaacctaactctatgttgtagttccagccttctgggttatgtt-tgttggaactaacttctgtttcaatcactattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA
||| |  ||     ||   |   || || |  || ||   |     | |  |||    ||   || ||   | || | | ||  || | |  |||||||||  ||||||||||||| || ||||| || || ||   ||||||||||||||| |||||||| ||||||||||| ||||| || || 
gtaagttgaatctatattgttcttccatttattaattgttggaaaatagtgtataacatgaccgatctttttcctctattaaatacaact-tagTGAGAGCCAACTTTGAGTTCATTGAAAAGCTTGGAGTCGATCTATGGTGCTTCCATGACAGGGATATAGCCCCTGATGGTAAAACCCTGGAG
















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|149080694|gb|EE169755.2|EE169755
EST:     TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAA                         TGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGGTGACAAATGGTGCT
genomic: TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAAgtatgaggat ... actattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCT
EST: gi|211302405|gb|FL012357.1|FL012357
EST:     TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAA                         TGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCT
genomic: TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAAgtatgaggat ... actattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCT
EST: gi|67027757|gb|CO456506.1|CO456506
EST:     TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAA                         TGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCT
genomic: TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAAgtatgaggat ... actattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCT
EST: gi|148979224|gb|EE026582.2|EE026582
EST:     TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAA                         TGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTG
genomic: TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAAgtatgaggat ... actattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTG
EST: gi|67019408|gb|CO448157.1|CO448157
EST:     TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAA                         TGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCT
genomic: TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAAgtatgaggat ... actattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCT
EST: gi|148950087|gb|EC895623.2|EC895623
EST:     TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAA                         TGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCT
genomic: TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAAgtatgaggat ... actattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCT
EST: gi|76286923|gb|DV026491.1|DV026491
EST:     TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAA                         TGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCT
genomic: TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAAgtatgaggat ... actattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCT
EST: gi|21389921|gb|BQ527970.1|BQ527970
EST:     TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAA                         TGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCT
genomic: TTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAAgtatgaggat ... actattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCT

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: 41 (upstream exon), 49 (downstream exon)
Score: 216

CACACGTTCCGTGGTACTGGTGCTGATCCTTTTGGTGCGCCTACAAAGGTTTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAAgtatgaggat ... actattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 230

CACACGTTCCGTGGTACTGGTGCTGATCCTTTTGGTGCGCCTACAAAGGTTTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAAgtatgaggat ... actattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 323

CACACGTTCCGTGGTACTGGTGCTGATCCTTTTGGTGCGCCTACAAAGGTTTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAAgtatgaggat ... actattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 342

CACACGTTCCGTGGTACTGGTGCTGATCCTTTTGGTGCGCCTACAAAGGTTTGGCCTTGGGAGGACGGCACAAATTCGTTGGCCATGGCTAAGAGAAGAAgtatgaggat ... actattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagccttctgggttatgtttgttggaactaacttctgtttcaatcactattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA
                         aactaac  putative branch site (score: 342)
            ttatgttt  TA-rich tract