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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCACATTTTGAGTACCACAAGAAAGCAATTACATCTATCGAGTGGAGTCCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccctctttaccttctccggtttggacgcgctgggtttctgaaatgccgtgcctagtatttgcttacacctctcctgaattgtttggatttag

Basic information

species Zea mays
transcript AC208327.4_FGT003
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC208327.4_FGT003 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os11g03990.1 (Oryza sativa), 5'ss of exon 11
TGGCACATTTTGAGTACCACAAGAAAGCAATTACATCTATCGAGTGGAGTCCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccctc----------tttac-cttctccggtttggacgcgctgggtttct------gaaatgccgtgcctagtattt----gcttacacctc----tcctgaattgtttggatttag
| || |||||||| ||||||||| |  ||||||||||| | || ||||| ||||||||| | ||| || |||||||| |||| |  || |||||||| |||||  || |            ||||  | | |  | ||     | ||||   | |        |||||   |   || |||||     ||| ||  |     ||||||||||||||  |  ||
TCGCCCATTTTGAATACCACAAGCACCCAATTACATCTGTGGAATGGAGCCCACATGAACCGTCAACACTAGCTGTATCATCAGCTGACCATCAACTGACgtaagtctcctcattccaagttttatacctttatgtttaaagtgtgctgaaatgccccaaaaaaaatgttttctttactattttctgacttgcatttttcaatcctgaattgtttgtgtacag

upper sequence: AC208327.4_FGT003 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA05G28040.2 (Glycine max), 5'ss of exon 11
TGGCACATTTTGAGTACCACAAGAAAGCAATTACATCTATCGAGTGGAGTCCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctc-----cctctttaccttctccggtttggacgcgctgggtttctgaaatgccgtgcctagtatttgcttacacctctcctgaattgtttggatttag--
| |||||||| || || |||||| |  |||| ||||| || |||||||||||||||||||| || |||||||| ||  | ||    ||| |||| || |||||  |        |   || | |   | | |         |  | || |  | ||   |       | ||  |   |      ||    | |||  | |||   
TAGCACATTTCGAATATCACAAGCACCCAATCACATCCATTGAGTGGAGTCCACATGAAGCCTCTTCATTAGCAGTTTCTTCATCTGATAATCAGCTTACgtaagtaaaggatattgatagcattatctgctgaattattttttgcttttatactgt--taatagagacttagtggtaaaaggtcta---tctttacacttatac
















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|20337018|gb|BQ172648.1|BQ172648
EST:     CCACATGTAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAAC                         AATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
EST: gi|78544326|gb|DV621824.1|DV621824
EST:     CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAAC                         AATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
EST: gi|32935721|gb|CF040533.1|CF040533
EST:     CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAAC                         AATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
EST: gi|37378418|gb|CF625898.1|CF625898
EST:     CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAAC                         AATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
EST: gi|33096363|gb|CF056357.1|CF056357
EST:     CCACATGAAGCATCATCATTAGCTGTAACATCCGAAGATCATCAACTAAC                         AATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
EST: gi|78545045|gb|DV622543.1|DV622543
EST:     CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAAC                         AATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
EST: gi|211303562|gb|FL306499.1|FL306499
EST:     CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAAC                         AATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
EST: gi|74242019|gb|DT649933.1|DT649933
EST:     CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAAC                         AATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
EST: gi|211412498|gb|FL461990.1|FL461990
EST:     CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAAC                         AATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
EST: gi|31349324|gb|CD433681.1|CD433681
EST:     CACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCACCTAAAC                         A-TCTGGGACCTTT
genomic: CACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAA-Cgtagctccct ... ttggatttagAATCTGGGACCTTT
EST: gi|19769952|gb|BQ034673.1|BQ034673
EST:     CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAAC                         AATCTGGGCCCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
EST: gi|50339077|gb|CO534203.1|CO534203
EST:     CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAAC                         AATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
EST: gi|211466441|gb|FL172132.1|FL172132
EST:     CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAAC                         AATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
EST: gi|21088827|gb|BQ401140.1|BQ401140
EST:     CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAAC                         AATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
genomic: CCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
EST: gi|211355147|gb|FL476248.1|FL476248
EST:     GCATCATCATTAGCTGT-ACATCTG-AGATCATCAACTAAC                         AATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG
genomic: GCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAG

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), 49 (downstream exon)
Score: 289

TGGCACATTTTGAGTACCACAAGAAAGCAATTACATCTATCGAGTGGAGTCCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAGAGCAAAGATGAAGGAGCAGGCAAACGCACCTGAAGATTTGCCCCCACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

TGGCACATTTTGAGTACCACAAGAAAGCAATTACATCTATCGAGTGGAGTCCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAGAGCAAAGATGAAGGAGCAGGCAAACGCACCTGAAGATTTGCCCCCACAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 183

TGGCACATTTTGAGTACCACAAGAAAGCAATTACATCTATCGAGTGGAGTCCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAGAGCAAAGATGAAGGAGCAGGCAAACGCACCTGAAGATTTGCCCCCACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

TGGCACATTTTGAGTACCACAAGAAAGCAATTACATCTATCGAGTGGAGTCCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccct ... ttggatttagAATCTGGGACCTTTCACTGGAAAGAGATGCGGAGGAGGAGGCTGAGTTCAGAGCAAAGATGAAGGAGCAGGCAAACGCACCTGAAGATTTGCCCCCACAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCACATTTTGAGTACCACAAGAAAGCAATTACATCTATCGAGTGGAGTCCACATGAAGCATCATCATTAGCTGTAACATCTGAAGATCATCAACTAACgtagctccctctttaccttctccggtttggacgcgctgggtttctgaaatgccgtgcctagtatttgcttacacctctcctgaattgtttggatttag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA