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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccagactattggtaccatctcacttttgtgcacggtacacacatagatacagtgaattctgatcctgtagcatccattcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG

Basic information

species Zea mays
transcript GRMZM5G801369_T02
intron # 13
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|56461966|gb|CK986264.1|CK986264
EST:     TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|4621622|gb|AI612455.1|AI612455
EST:     TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|32838018|gb|CD977696.1|CD977696
EST:     TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|78120790|gb|DV539174.1|DV539174
EST:     TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|32837052|gb|CD976730.1|CD976730
EST:     TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|6021059|gb|AW065987.1|AW065987
EST:     TTGACTCCCAGTGGATTGGTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|6601788|gb|AW256229.1|AW256229
EST:     TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|211502844|gb|FL437375.1|FL437375
EST:     TTGATTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|32917091|gb|CF021903.1|CF021903
EST:     TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|211325390|gb|FL371043.1|FL371043
EST:     TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|18164577|gb|BM334416.1|BM334416
EST:     TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|50331568|gb|CO526694.1|CO526694
EST:     TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|32838737|gb|CD978418.1|CD978418
EST:     TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|32832999|gb|CD972677.1|CD972677
EST:     TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|12973204|gb|BG268364.1|BG268364
EST:     TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG                         GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG

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), 43 (downstream exon)
Score: 10

CCAGCCCATGAGAAAATTGGAGTGGTTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG


Block sizes: 44 (upstream exon), 41 (downstream exon)
Score: 16

CCAGCCCATGAGAAAATTGGAGTGGTTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 33

CCAGCCCATGAGAAAATTGGAGTGGTTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 35

CCAGCCCATGAGAAAATTGGAGTGGTTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccaga ... ttcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggtacacacatagatacagtgaattctgatcctgtagcatccattcctgtcagGGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG
                         ttctgat  putative branch site (score: 35)
                                         tccattcct  putative PPT
           atagata  TA-rich tract