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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGCGGAGGCCTTGGAGGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa

Basic information

species Zea mays
transcript GRMZM2G088834_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088834_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g04814.1 (Oryza sativa), 5'ss of exon 2
GCAAGCGGAGGCCTTGGAGGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa-----------------------------------------------------------------------------------------------------------------------------------------
      |||| || |||||||| |||||||||||||| || |||||||||||||||||||||||||| |                                                                                                                                         
------GGAGACCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAGGAAAGTCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATTTTTCAGgtagttataccctcatatatatacctatatatttcaactacatatcttgacaataaatcctcactcttactaattccattactaaaactcaatgacgtgg

upper sequence: GRMZM2G088834_T03 (Zea mays), 5'ss of exon 2
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 5'ss of exon 2
GCAAGCGGAGGCCTTGGAGGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa-----------------------------------------------------------------------------------------------------------------------------------------
      |  |||||||||| || ||||| |||||||| || || ||||||||||| || |||||||| |                                                                                                                                         
------GACGGCCTTGGAGAGCTTTTCTGTTGTATGGGCCTCCTGGAACAGGAAAATCGTATTTGGCTAAGGCTGTTGCCACTGAAGCTGACTCTACCTTTTTTAGgtaacgtatgtttaaaagtgtttgaatttctgaaagtatataggaagaggatggtgtagtgtcttaactctttcattatagcttgagaccatagtcaaat

upper sequence: GRMZM2G088834_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv13s0106g00490.t01 (Vitis vinifera), 5'ss of exon 2
GCAAGCGGAGGCCTTGGAGGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa-----------------------------------------------------------------------------------------------------------------------------------------
      |  |||| |||||||| ||||| |||||||| || || |||||||||||||| || || || |                                                                                                                                         
------GACGGCCCTGGAGGGCTTTTCTATTGTATGGTCCACCTGGAACAGGAAAGTCATACTTAGCCAAGGCTGTTGCAACAGAAGCAGACTCAACATTCTTCAGgtagcatattcataatcatctaaaattagccgtttactttactatagcagatacaaagctagtaagcatctatttcataagcaatcctggactccagtta

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|87157780|gb|DY402569.1|DY402569
EST:     GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCA                         AAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAG
genomic: GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa ... aAAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAGgtagatagtt ... ttt
EST: gi|31353555|gb|CD437912.1|CD437912
EST:     GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCA                         AAAGCTGTTGCAACCGAGGCTGATTC
genomic: GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa ... aAAAGCTGTTGCAACCGAGGCTGATTC
EST: gi|76015516|gb|DT942686.1|DT942686
EST:     GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCA                         AAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAG
genomic: GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa ... aAAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAGgtagatagtt ... ttt
EST: gi|22935971|gb|BU572246.1|BU572246
EST:     GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCA                         AAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAG
genomic: GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa ... aAAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAGgtagatagtt ... ttt
EST: gi|148983029|gb|EE028935.2|EE028935
EST:     GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCA                         AAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAG
genomic: GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa ... aAAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAGgtagatagtt ... ttt
EST: gi|148947377|gb|EC892780.2|EC892780
EST:     GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCA                         AAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAG
genomic: GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa ... aAAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAGgtagatagtt ... ttt
EST: gi|148964892|gb|EE015751.2|EE015751
EST:     GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCA                         AAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAG
genomic: GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa ... aAAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAGgtagatagtt ... ttt
EST: gi|71325163|gb|DR799271.1|DR799271
EST:     GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCA                         AAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAGTATATCT
genomic: GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa ... aAAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAGTATATCT
EST: gi|149089679|gb|EE178936.2|EE178936
EST:     GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCA                         AAAGCTGTTGCAACCGAGGCTGATTCCACGTTTTTCAG
genomic: GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa ... aAAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAGgtagatagtt ... ttt
EST: gi|26559939|gb|CA832174.1|CA832174
EST:     GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCA                         AAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAG
genomic: GGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa ... aAAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAGgtagatagtt ... ttt

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), 49 (downstream exon)
Score: 381

GCAAGCGGAGGCCTTGGAGGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa ... aAAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 523

GCAAGCGGAGGCCTTGGAGGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa ... aAAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAG


Block sizes: 48 (upstream exon), 38 (downstream exon)
Score: 478

GCAAGCGGAGGCCTTGGAGGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa ... aAAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 437

GCAAGCGGAGGCCTTGGAGGGCGTTTCTTTTGTATGGCCCCCCAGGAACAGGAAAGTCTTATTTGGCAa ... aAAAGCTGTTGCAACCGAGGCTGATTCAACGTTTTTCAG