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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgctttaacctgaatccctgtatgttagtacctaacttcatatctcacatgtgcagtgagtgttatgtgttttcttctcctgttttggaaccac...

Basic information

species Zea mays
transcript GRMZM2G044629_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044629_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 4
GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgctttaacctgaatccctgtatgttagtacctaacttcatatctcacatgtgcagtgagtgttatgtgttttcttctcctgttttggaaccac--
|| ||||| || || ||||| |||||||| |||||||||||||||||| ||  || | ||||  ||||| ||||||| | | ||  || | ||||  || | ||  | ||   ||               |  |   | |  
GGGACTCGGCTTGGTAGCTCTGATCCTAAAGGATGTTTCAgtaagttgattccacttcaatctttgtatattagtacttgagtttgta-cgcacaaatgta-tggatatttgttgagccaaaaaaagaagtgaggtgctctg
















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|149081508|gb|EE170644.2|EE170644
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|211249747|gb|FL285802.1|FL285802
EST:     GGTACTCGACTGGGAAGCTCAGATCCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGG
genomic: GGTACTCGACTGGGAAGCTCAGATCC-TAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGG-
EST: gi|149015643|gb|EE045441.2|EE045441
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|40337292|gb|CK371362.1|CK371362
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|149100896|gb|EE186991.2|EE186991
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCCAGCTGAAAG
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAG
EST: gi|149014175|gb|EE043721.2|EE043721
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|148958334|gb|EC904558.2|EC904558
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|71429565|gb|DR810615.1|DR810615
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|148982619|gb|EE028417.2|EE028417
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|211249751|gb|FL285806.1|FL285806
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCNNAGCTGAA-GG
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCA-AGCTGAAAGG
EST: gi|149090039|gb|EE179333.2|EE179333
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|78115803|gb|DV534191.1|DV534191
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCCGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|148956834|gb|EC902742.2|EC902742
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|91052249|gb|EB162667.1|EB162667
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|149014877|gb|EE044588.2|EE044588
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|148943648|gb|EC888712.2|EC888712
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|71757247|gb|DR955184.1|DR955184
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|148990989|gb|EE032426.2|EE032426
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|94477177|gb|EB706135.1|EB706135
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|31354041|gb|CD438398.1|CD438398
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
EST: gi|76282035|gb|DV021603.1|DV021603
EST:     GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA                         ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA
genomic: GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGA

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: 40 (upstream exon), 48 (downstream exon)
Score: 183

GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 314

GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 310

GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 643

GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgct ... tttgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgctttaacctgaatccctgtatgttagtacctaacttcatatctcacatgtgcagtgagtgttatgtgttttcttctcctgttttggaaccac

- - - - - - -  AGCTCA