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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggtgactgctcaacgagtcctacatccttcagattctcgtttgagtttgtgcttaactatttctcatacaatggatatctcttcagGACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG

Basic information

species Zea mays
transcript GRMZM5G814279_T02
intron # 5
splice site 3'
intron type U2

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|60359649|gb|DN226622.1|DN226622
EST:     GAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAG                         GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG
genomic: GAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAGgtagggtgac ... atctcttcagGACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG
EST: gi|60341355|gb|DN208328.1|DN208328
EST:     GAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAG                         GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG
genomic: GAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAGgtagggtgac ... atctcttcagGACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG
EST: gi|166464309|gb|EG188249.1|EG188249
EST:     GAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAG                         GACCAGCTATTCATGCAACAAATCGGCGAATTAC
genomic: GAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAGgtagggtgac ... atctcttcagGACCAGCTATTCATGCAACAAATCGGCGAATTAC
EST: gi|91871951|gb|EB401908.1|EB401908
EST:     GGAAAGGAAACTTGAAGCAGGGCCGCATAGAGTGATTAGTACAAAG                         GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG
genomic: GGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAGgtagggtgac ... atctcttcagGACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG
EST: gi|91871952|gb|EB401909.1|EB401909
EST:     GAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAG                         GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG
genomic: GAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAGgtagggtgac ... atctcttcagGACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG
EST: gi|71312209|gb|DR792627.1|DR792627
EST:     GAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAG                         GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG
genomic: GAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAGgtagggtgac ... atctcttcagGACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG
EST: gi|60355305|gb|DN222278.1|DN222278
EST:     GAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAG                         GACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG
genomic: GAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAGgtagggtgac ... atctcttcagGACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG

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), 49 (downstream exon)
Score: 42

ACAGATGAGAGGTGAAGACCTTGAGGGATTGAGTGTAGAGGAATTGCACCGAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAGgtagggtgac ... atctcttcagGACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 12

ACAGATGAGAGGTGAAGACCTTGAGGGATTGAGTGTAGAGGAATTGCACCGAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAGgtagggtgac ... atctcttcagGACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 10

ACAGATGAGAGGTGAAGACCTTGAGGGATTGAGTGTAGAGGAATTGCACCGAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAGgtagggtgac ... atctcttcagGACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 5

ACAGATGAGAGGTGAAGACCTTGAGGGATTGAGTGTAGAGGAATTGCACCGAATGGAAAGGAAACTTGAAGCAGGACTGCATAGAGTGATTAGTACAAAGgtagggtgac ... atctcttcagGACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattctcgtttgagtttgtgcttaactatttctcatacaatggatatctcttcagGACCAGCTATTCATGCAACAAATCGGCGAATTACTGCAAAAG
                   gcttaac  putative branch site (score: 5)
                                            tatctcttc  putative PPT
                     ttaactattt  TA-rich tract