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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgcaacttttcaattttattatgctgaagtatgtatgttaacatctctgttctgctttgtgctctatag

Basic information

species Zea mays
transcript GRMZM2G074373_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074373_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os12g13170.1 (Oryza sativa), 5'ss of exon 12
TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgtt-gacctgcaacttttcaattt--tattatgctgaagtatgtatgttaacatctctgttctgctttgtgctctatag
|||||| ||||||||||| |||||| ||||||||||||||||||| ||||| |||||||| |||||||| || ||||||||||||||||  ||| |||||||| |   |   | | |||  | |  |  ||| ||||| ||| ||  ||||||    |  | || ||| || ||| |||
TGCTGAAGTTTTAAAGCAAGAAAATACTTCACTTAGAGATGAAGTGAACCGGATCAGAAAGGAGTATGATGAGCTTCTATCAAAGAATAGCTCATTAAAGgtttggtttctcattcttcgctctcttgctattctgaaatatatactttaacactgtt--tttgttttttgttctgtag
















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|78090596|gb|DV518970.1|DV518970
EST:     GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|94479027|gb|EB707985.1|EB707985
EST:     GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGGGGCAGGGCTTAACAAC
genomic: GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|6994170|gb|AW453384.1|AW453384
EST:     GGAACTTCTATCAAAGAA-AATTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|211196022|gb|FL462720.1|FL462720
EST:     AGAATAATTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: AGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|31358760|gb|CD443117.1|CD443117
EST:     GTATCAGAAAAGAGTATGAGGAACTTGTATCAAAGAATAATTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|149110852|gb|EE294350.2|EE294350
EST:     GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|211028676|gb|FL452179.1|FL452179
EST:     GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|211028675|gb|FL452178.1|FL452178
EST:     GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|71318159|gb|DR795842.1|DR795842
EST:     GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|60345262|gb|DN212235.1|DN212235
EST:     GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|60399438|gb|DN232250.1|DN232250
EST:     GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|89251780|gb|DY623566.1|DY623566
EST:     GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|110190661|gb|EC872559.1|EC872559
EST:     GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCATTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|60337421|gb|DN204394.1|DN204394
EST:     AAAGAATAATTCACGGAAG                         GAAAAACTGGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: AAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|40485763|gb|CK394726.1|CK394726
EST:     GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
EST: gi|24766396|gb|CA401550.1|CA401550
EST:     GTATCAGAAAAGAGTATGAGGAACTTGTATCAAAGAATAATTCACTAAAG                         GAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC
genomic: GTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAAC

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), 44 (downstream exon)
Score: 63

TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAACAAGCTGCAACATTCTGGCAATGACATCCAGAAAAAAGGAAACTAATCGA


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 25

TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAACAAGCTGCAACATTCTGGCAATGACATCCAGAAAAAAGGAAACTAATCGA


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 44

TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAACAAGCTGCAACATTCTGGCAATGACATCCAGAAAAAAGGAAACTAATCGA


Block sizes: 48 (upstream exon), 22 (downstream exon)
Score: 50

TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgc ... tgctctatagGAAAAACTTGAAGGCAAACAACACAAAACTGATGAGGCAGGACTTAACAACAAGCTGCAACATTCTGGCAATGACATCCAGAAAAAAGGAAACTAATCGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAACTTCTATCAAAGAATAATTCACTAAAGgttgacctgcaacttttcaattttattatgctgaagtatgtatgttaacatctctgttctgctttgtgctctatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA