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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtccctgatgtcatttgtttctcattctgtgaaaaaggatgatctctgattaaaagtggagttaaaccaacatggtattcttctgtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGGAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG

Basic information

species Zea mays
transcript GRMZM2G005493_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 17
gtcagtccctgatgtcatttgtttctcattctgtgaaaaagga---tgatctctgattaaaagtggagttaaaccaacatggtattcttctgtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGGAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG
||  || || | || ||||  ||| |  || ||||     | |   || ||||||||| ||  || | || ||   || ||| |||||  | ||   ||||| ||||||| || ||||||||||||||| ||||||| |||||||| || |||||||||||||| ||||| ||||| || || |  | |||||||||||||
gttggttcccgctgacattgttttttttttttgtgtgtgtgtaaattggtctctgattcaac-tgaatttcaattgacttggaattctattatgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGGAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG

upper sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 18
-------------------------------gtcagtccc-tgatgtcatttgtttctcattctgtgaaaa-----aggatgatctctgattaaaagtggagttaaaccaacatggtattcttctgtga-tgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGGAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG
                                | | |    | ||||  ||||||| |   | |||          |  |     | ||  |            | || | | |  | || || | ||| |   ||||| ||||| |||||||||||||||||  | ||  || |||| ||    ||||||||||||||||||||||| ||||| || |  || ||  | || |||
gtaagtttctttcttttttgtttatatggaccttatttttataatgttgtttgtttgtttgtttgtttgttttttcaatacttcttatgcctctggagattaccatactatcttcatttttttttatgaattttagGCGAAGGGAGAGCACTGATGTTGAGGATCTCTTCATTTCTCACATTAGTGGAATGGACACCCTGGCCCGTGGTCTCCGAAATGTTGCTAAATTAATTGAG
















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|60337180|gb|DN204153.1|DN204153
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|29130773|gb|CB381477.1|CB381477
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|76286922|gb|DV026490.1|DV026490
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|211174464|gb|FL381682.1|FL381682
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|60344318|gb|DN211291.1|DN211291
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|32836432|gb|CD976110.1|CD976110
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|211379703|gb|FL400539.1|FL400539
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|32844741|gb|CD984422.1|CD984422
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|32845281|gb|CD984962.1|CD984962
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|213179445|gb|FM183428.1|FM183428
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|33097350|gb|CF057310.1|CF057310
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|32838372|gb|CD978050.1|CD978050
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTACGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|32845336|gb|CD985017.1|CD985017
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|37385849|gb|CF630089.1|CF630089
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|60346929|gb|DN213902.1|DN213902
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|32935034|gb|CF039846.1|CF039846
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|211459151|gb|FL411539.1|FL411539
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|32844417|gb|CD984098.1|CD984098
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|211214717|gb|FL394674.1|FL394674
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|60337495|gb|DN204468.1|DN204468
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|67037452|gb|CO464268.1|CO464268
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|32844874|gb|CD984555.1|CD984555
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|6012630|gb|AW062067.1|AW062067
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|32838758|gb|CD978439.1|CD978439
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|60353702|gb|DN220675.1|DN220675
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|110219847|gb|EC901745.1|EC901745
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATTTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|74244418|gb|DT652332.1|DT652332
EST:     TTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: TTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|67010832|gb|CO439581.1|CO439581
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|32837235|gb|CD976913.1|CD976913
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
EST: gi|60347419|gb|DN214392.1|DN214392
EST:     GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATT                         GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGG

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: 272

GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGGAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 335

GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGGAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 270

GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGGAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 445

GGTGGACTTGCACCTGGTGGCTTCAACTTTGACGCCAAATTgtcagtccct ... gtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGGAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatctctgattaaaagtggagttaaaccaacatggtattcttctgtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGGAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG
    ctctgat  putative branch site (score: 445)
                                      ttcttctgt  putative PPT
       tgattaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtccctgatgtcatttgtttctcattctgtgaaaaaggatgatctctgattaaaagtggagttaaaccaacatggtattcttctgtgatgacagGCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGGAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT