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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGCCCATGAGAAAATTGGAGTGGTTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccagactattggtaccatctcacttttgtgcacggtacacacatagatacagtgaattctgatcctgtagcatccattcctgtcag

Basic information

species Zea mays
transcript GRMZM5G801369_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G801369_T03 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA12G29800.1 (Glycine max), 5'ss of exon 13
CCAGCCCATGAGAAAATTGGAGTGGTTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgt-atgccagactattggtaccatctcacttttgtgcacggtacacacatagatacagtgaattctgatcctgtagcatcc---attcctgtcag--------
||||| ||||| |||||||| ||  |||| || || ||||||||||||||||| || ||||| ||||| |||||||| |  ||  ||||  | |  ||    | ||  |  |||  ||    | | |||    | | ||   ||   ||    |     ||   |||  |        
CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAGgttagacctcacta--gcttacaatatagttagggccact-tattttctttgatgatatcattttaaattgagtgtgtttttatatatttgttgggagtatat

upper sequence: GRMZM5G801369_T03 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA13G39990.1 (Glycine max), 5'ss of exon 13
CCAGCCCATGAGAAAATTGGAGTGGTTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccag-actattggtaccatctcacttttgtgcacggtacacacatagatacagtgaattctgatcctgtagcatcc---attcctgtcag--------
||||| ||||| |||||||| ||  |||| || || ||||||||||||||||| || ||||| ||||| ||||||||  | ||  ||||    ||| || |    || | ||    ||    | | |||    | | ||   ||   | |   |     ||   | |  |        
CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAGgttagacatcactagct-tacaatatag--ttagagccacttattttctttgatgatatcattttaaattgagcatgtttttatatatttattgggagtatat
















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


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGCCCATGAGAAAATTGGAGTGGTTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAGgtatgccagactattggtaccatctcacttttgtgcacggtacacacatagatacagtgaattctgatcctgtagcatccattcctgtcag

- - - - - - - - - - - - - - - - - AGTGGA