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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatactaacatacgtgctattatgcattttctcattactcaaccatcgaacttgttttgatggaccattttaattgcttactcag

Basic information

species Zea mays
transcript GRMZM2G059671_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059671_T04 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 15
GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatactaacatacgtgctattatgcattttctcattactcaaccatcgaacttgttttgatggaccattttaattgcttactcag
|| || ||||| |||||||| || || | ||||||||| || ||||| ||||||||||| |||||||||||| |||| || |||||||||   | || |     ||| |||| || ||| |||  | ||||||  |||     | | || ||| ||||||| |  |||||| ||   |   |||
GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtat--ctataatatac-tgttat-atgtttcttctcacaacttg--tagccaagttggtttgatgaat-attttatttttatttgcag
















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|19770366|gb|BQ035087.1|BQ035087
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|19822326|gb|BQ048350.1|BQ048350
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|76284240|gb|DV023808.1|DV023808
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|26456039|gb|CA827622.1|CA827622
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|67042437|gb|CO468692.1|CO468692
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGTCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|149096725|gb|EE182499.2|EE182499
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|113703759|gb|EE681263.1|EE681263
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGTCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|88757722|gb|DY541863.1|DY541863
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|20336958|gb|BQ172588.1|BQ172588
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|78110653|gb|DV529058.1|DV529058
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|60358265|gb|DN225238.1|DN225238
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|60357002|gb|DN223975.1|DN223975
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|60337361|gb|DN204334.1|DN204334
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|148945985|gb|EC891279.2|EC891279
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|211160526|gb|FL223272.1|FL223272
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|19770367|gb|BQ035088.1|BQ035088
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|78544160|gb|DV621658.1|DV621658
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
EST: gi|78544345|gb|DV621843.1|DV621843
EST:     AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAG                         GGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT
genomic: AGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACT

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 1 RNA-Seqlibrary.


Block sizes: 19 (upstream exon), 31 (downstream exon)
Score: 2

GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatact ... gcttactcagGGAGCCCTGGAGACGACCCTCTTTTGCCAGTATCATGGAATCCCTGAAACTTCTCATCAAGACATTACCACCCAATCAGCTCCTCGAAGAAAATTAGTTA




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