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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGAAAGTATTACAACGCATCCATCGATTACCAAATAGAGTTTTACAGAAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaactcatcagattatggtaataacgtcgcttcagtttcttgctggaaatcctaatgctgagcggccccttttgcttggcatgcag

Basic information

species Zea mays
transcript GRMZM2G421791_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421791_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g45490.1 (Oryza sativa), 5'ss of exon 7
GCTGGAAAGTATTACAACGCATCCATCGATTACCAAATAGAGTTTTACAGAAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaactcatcagattatggtaataacgtcgcttcagtttcttgctggaaatcctaatgctgagcggccccttttgc-ttggcatgcag
||||| |||||| |||| ||||| || ||||||||||||||||||||| ||||||||||||||||| ||||| | ||||| |||||||| || ||||||||||||||| |||||   | |||||  | |||     ||||||| ||| ||| | ||  |||       | | || |||||| ||||  |    
GCTGGCAAGTATGACAATGCATCAATTGATTACCAAATAGAGTTTTACCGAAATGAGGGCCTAACATATTATACACCTGCTAAGCTTCCTATTACAAGTGgtcagtgatctcattgaagtatggcgaaaacag---ttcagttactttctg-agattttaa-------ctgtcctttttgcattggtttag--
















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|71439406|gb|DR820456.1|DR820456
EST:     AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAGGTG                         ATGTCTCTGAAAGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
genomic: AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
EST: gi|33096912|gb|CF056872.1|CF056872
EST:     AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTG                         ATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
genomic: AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
EST: gi|33099543|gb|CF059503.1|CF059503
EST:     AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTG                         ATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
genomic: AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
EST: gi|13149974|gb|BG320296.1|BG320296
EST:     AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTG                         ATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
genomic: AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
EST: gi|149096257|gb|EE181965.2|EE181965
EST:     CAAGCTCCCCATCACAAGTG                         ATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
genomic: CAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
EST: gi|31357415|gb|CD441772.1|CD441772
EST:     AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTG                         ATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
genomic: AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
EST: gi|16921217|gb|BM075042.1|BM075042
EST:     AAATGAGGGCNTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTG                         ATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
genomic: AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
EST: gi|211234336|gb|FL414451.1|FL414451
EST:     AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTG                         ATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
genomic: AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
EST: gi|87156073|gb|DY400862.1|DY400862
EST:     AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTG                         ATGTCCCTGAAAGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
genomic: AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
EST: gi|149087532|gb|EE176930.2|EE176930
EST:     AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTG                         ATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
genomic: AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
EST: gi|149097874|gb|EE183808.2|EE183808
EST:     AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTG                         ATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC
genomic: AAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACC

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: 46 (upstream exon), 48 (downstream exon)
Score: 37

GCTGGAAAGTATTACAACGCATCCATCGATTACCAAATAGAGTTTTACAGAAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACCTCTTCACGTGCTTATGGTTCAATGAAGTTGATCGCTTCACCTCCAGGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

GCTGGAAAGTATTACAACGCATCCATCGATTACCAAATAGAGTTTTACAGAAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACCTCTTCACGTGCTTATGGTTCAATGAAGTTGATCGCTTCACCTCCAGGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 124

GCTGGAAAGTATTACAACGCATCCATCGATTACCAAATAGAGTTTTACAGAAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACCTCTTCACGTGCTTATGGTTCAATGAAGTTGATCGCTTCACCTCCAGGGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 148

GCTGGAAAGTATTACAACGCATCCATCGATTACCAAATAGAGTTTTACAGAAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaac ... tggcatgcagATGTCCCTGAAGGCTGTGTGATCATCAGAGAACACATCCCCATCACGAACCTCTTCACGTGCTTATGGTTCAATGAAGTTGATCGCTTCACCTCCAGGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGAAAGTATTACAACGCATCCATCGATTACCAAATAGAGTTTTACAGAAATGAGGGCCTAACACATTATTCTCCTGCCAAGCTTCCCATCACAAGTGgtcagtgaactcatcagattatggtaataacgtcgcttcagtttcttgctggaaatcctaatgctgagcggccccttttgcttggcatgcag

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