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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGACATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtccatttcttttcttctttgttcactttagtggatagttagctatatactgattattatgaaatttgcttatctactgctgtctggcag

Basic information

species Zea mays
transcript GRMZM2G008556_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008556_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 5'ss of exon 9
TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGACATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtccatttcttttcttctttgttcactttagtggatagttagctatatactgattattatgaaatttgcttatctactgctgtctggcag
|||||| || ||||||||| |||| || ||||||||||||||||||||| |||||||||| || ||||||| ||||||||||||||||||||| |||||||| ||     ||||   | ||| ||||||    | |||  ||||  ||||  |||       |||  |||||| | | | |  |  ||||   |||
TGGTTTTCTTTATGATATGTTGCAGAAGGAGGTAATTTCTTTGAGAAAGGCATGCCATGAAAAAGATCAGAGTCTAAAAGATAAAGATGATGCGATTGAGgtatggaaatattt---tgcttatttgttgcactgagttcataggaagctcgata-------ttagaaaatttacctgtttcttcttgtcctacag

upper sequence: GRMZM2G008556_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 9
TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGACATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtccatttcttttcttctttgttcactttag---tggatagttagctatatac--tgattattatgaaatttgcttatctactgctgtctggcag
  || |  |||||||  | |||||||||||||| ||  | ||||| ||  |  | || ||||| ||||| |  |||||||||||||||||||||||||||||  ||||    |   ||| || | | |  |  | |    ||  |  |||  |||| |   |  |  ||   || | |    |          |||  |||
CAGTGTTTTATATGACTTTCTGCAAAAAGAGGTCATAGCCTTGAGGAAAGCTGGTCACGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCTATTGAGgtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcag

upper sequence: GRMZM2G008556_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGACATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtccatttcttt-tcttctttgtt-cactttagtggatagttagctatatactgattattatgaaatttgcttatctactgctgtctggcag
 ||  |  |||||||||||||||||||||||||  |||||||||| ||  |  | ||||| || ||||| |  || |||||||| |||||||||||||||||  || | | | || |  |||   || |    ||||| |  ||| ||   |    |   |||   ||| ||||  ||| |  |              
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggtattcttgtcctcatctgtcttatgatgctttaattcatattt--ttgctcatgtatttggatgtaatt--ctttttcag-------------

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|60355070|gb|DN222043.1|DN222043
EST:     CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
genomic: CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
EST: gi|71426784|gb|DR807834.1|DR807834
EST:     CATGCCATGAGAAGGATCAGATTTTAAAAGATAAAGAGGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGCCACCTTAACTAAAGCAATGGAAGTGGAAGCT
genomic: CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
EST: gi|113703080|gb|EE680584.1|EE680584
EST:     CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
genomic: CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
EST: gi|71762835|gb|DR960772.1|DR960772
EST:     CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
genomic: CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
EST: gi|32838182|gb|CD977860.1|CD977860
EST:     CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
genomic: CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
EST: gi|5739791|gb|AI947367.1|AI947367
EST:     CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACNCCTTAACTAAAGCAATGGAAGTGGAAGCT
genomic: CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
EST: gi|211220743|gb|FL455239.1|FL455239
EST:     AGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
genomic: AGATGATGCTATTGAGgtctgtgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
EST: gi|6021554|gb|AW066482.1|AW066482
EST:     CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
genomic: CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
EST: gi|32837805|gb|CD977483.1|CD977483
EST:     CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATNATNCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT
genomic: CATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 499

TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGACATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCTAAAAAGGTCAGACGGGAGGTTGCATCCATGGAGAAAGAAGTTGCAGCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 204

TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGACATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCTAAAAAGGTCAGACGGGAGGTTGCATCCATGGAGAAAGAAGTTGCAGCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 158

TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGACATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCTAAAAAGGTCAGACGGGAGGTTGCATCCATGGAGAAAGAAGTTGCAGCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 269

TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGACATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACTAAAGCAATGGAAGTGGAAGCTAAAAAGGTCAGACGGGAGGTTGCATCCATGGAGAAAGAAGTTGCAGCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGACATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtccatttcttttcttctttgttcactttagtggatagttagctatatactgattattatgaaatttgcttatctactgctgtctggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG