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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaacgcagtgcacagtaactgatttctttttatataataaatgcacgattgatatatacaagcttgctcgcag

Basic information

species Zea mays
transcript GRMZM2G113726_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113726_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os08g38880.6 (Oryza sativa), 5'ss of exon 7
CATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaacgcagtgcacagtaactgatttct---------ttttatat---aataaatgcacgattgatatatacaagcttgctcgcag
|| ||||| |||||||| ||||||||||||| ||||||||| |||||||  ||||| |||||| |  | ||  ||||||||||||| |||||| ||| |||  || |||  | | | |||            | | ||   |  ||| | |    | ||   |    | || |||||||
CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaaagcaacgctcagcgattaacttccaaatactgacctcacatttcagaaaaagaaaagctcatggctgtttgttt-ctcgcag

upper sequence: GRMZM2G113726_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os08g38880.3 (Oryza sativa), 5'ss of exon 7
CATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaacgcagtgcacagtaactgatttct---------ttttatat---aataaatgcacgattgatatatacaagcttgctcgcag----
|| ||||| |||||||| ||||||||||||| ||||||||| |||||||  ||||| |||||| |  | ||  ||||||||||||| |||||| ||| |||  || |||  | | | |||            | | ||   |  ||| | |    | ||   |    | || |||||||    
CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaaagcaacgctcagcgattaacttccaaatactgacctcacatttcagaaaaagaaaagctcatggctgtttgttt-ctcgcagacag
















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|18167290|gb|BM337129.1|BM337129
EST:     TGT-GGGGACCAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
genomic: TGTGGGGGA-CAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
EST: gi|50330987|gb|CO526113.1|CO526113
EST:     TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
genomic: TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
EST: gi|56461997|gb|CK986295.1|CK986295
EST:     TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
genomic: TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
EST: gi|47961405|gb|CN844114.1|CN844114
EST:     TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGTTCANAA-CTCCATGGCCATTTGGATTACTCCNTTGCGTCGGCATGG
genomic: TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
EST: gi|44681734|gb|CK786782.1|CK786782
EST:     TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
genomic: TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
EST: gi|44682058|gb|CK787106.1|CK787106
EST:     TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGNTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
genomic: TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
EST: gi|47962732|gb|CN845441.1|CN845441
EST:     TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
genomic: TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
EST: gi|78024436|gb|DV492823.1|DV492823
EST:     TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
genomic: TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG

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 2 RNA-Seq libraries.


Block sizes: 37 (upstream exon), 13 (downstream exon)
Score: 1

CATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGGAATCCAGACGGCCGAACATTCGCCACGGGGAACCAAGACAAGACGTGCA


Block sizes: 37 (upstream exon), 13 (downstream exon)
Score: 1

CATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGGAATCCAGACGGCCGAACATTCGCCACGGGGAACCAAGACAAGACGTGCA




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaacgcagtgcacagtaactgatttctttttatataataaatgcacgattgatatatacaagcttgctcgcag

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