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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcactctgtcgatgctatatgtatttgtttttctgttgtgatttgtttttctgttgtgattacatatgtacttgcctaatgaataactgtttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCATTTCCACTTTGCTCCAAAGCCA

Basic information

species Zea mays
transcript GRMZM2G005308_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005308_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g04010.1 (Oryza sativa), 3'ss of exon 8
tcactctgtcgatgctatatgtatttgtttttctgttgtgatttgtttttctgttgtga--ttacatatgtact-tgcctaatgaataactgtttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCATTTCCACTTTGCTCCAAAGCCA
  | | |||     | || |  ||| ||  ||      | |||| ||   ||||  |||  ||  |    | ||      |   ||    |||||| || ||||||||||| ||||||||||| ||||| ||||| |||||||| ||||| ||||||||||||||||||||||| 
-aaatttgttcccaccattt-cattggtgctttatgcat-attttttcccctgtaatgatattggaggcttgctgcattgacctaacttttgtttccacttagGCAAATACCTTATTTAAGAGAATATGCTTGAAGTTGGATGCACTATCTCATTTCCACTTTGCTCCAAAGCCG

upper sequence: GRMZM2G005308_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g04200.1 (Oryza sativa), 3'ss of exon 8
tcactctgtcgatgctatatgtatttgtttttctgttgtgatttgtttttctgttgtga--ttacatatgtact-tgcctaatgaataactgtttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCATTTCCACTTTGCTCCAAAGCCA
  | | |||     | || |  ||| ||  ||      |  ||| ||   ||||  |||  ||| |    | ||      |   ||   ||||||| || |||||||| || ||||||||||| ||||| ||||| |||||||| ||||| ||||||||||||||||||||||| 
--aatttgttcccaccattt-cattggtgctttatgcatatttttttcccctgtgatgatattagaggcttgctgcattgacctaacttctgtttccacttagGCAAAGACCTTATTTAAGAGAATATGCTTGAAGTTGGATGCACTATCTCATTTCCACTTTGCTCCAAAGCCG
















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|60347217|gb|DN214190.1|DN214190
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|211462206|gb|FL207483.1|FL207483
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|211459691|gb|FL207478.1|FL207478
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|24769907|gb|CA405036.1|CA405036
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|211183290|gb|FL434310.1|FL434310
EST:     AGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: AGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|60394413|gb|DN227283.1|DN227283
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|71764578|gb|DR962515.1|DR962515
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|71761969|gb|DR959906.1|DR959906
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|211183291|gb|FL434311.1|FL434311
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|31364214|gb|CD448569.1|CD448569
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|211462204|gb|FL207481.1|FL207481
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|76011806|gb|DT938976.1|DT938976
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|40303495|gb|CK347882.1|CK347882
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
EST: gi|37392792|gb|CF633649.1|CF633649
EST:     CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAG                         GCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT
genomic: CAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCAT

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), 48 (downstream exon)
Score: 425

GATGACTATGCACAAAAAGCAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCATTTCCACTTTGCTCCAAAGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

GATGACTATGCACAAAAAGCAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCATTTCCACTTTGCTCCAAAGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 350

GATGACTATGCACAAAAAGCAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCATTTCCACTTTGCTCCAAAGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

GATGACTATGCACAAAAAGCAGGCATTGCACCTGCCCCACTTTCTATTTCAGATGAACTAAAGGAAGAGgtgagtaatt ... ttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCATTTCCACTTTGCTCCAAAGCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctgttgtgattacatatgtacttgcctaatgaataactgtttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCATTTCCACTTTGCTCCAAAGCCA
                                   gaataac  putative branch site (score: 260)
                                            tttctacct  putative PPT
                               taatgaataa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcactctgtcgatgctatatgtatttgtttttctgttgtgatttgtttttctgttgtgattacatatgtacttgcctaatgaataactgtttctacctagGCAAATACTTTATTTAAGAGGATATGTTTGAAATTGGATGCGCTATCGCATTTCCACTTTGCTCCAAAGCCA

- - - - - gatgcta
- - - - - - - - -tatgtat
- - - - - - - - - - - - -tgttttt
- - - - - - - - - - - - - - - - ctgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacttgc