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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGTCATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtccatttctttccttattcgttcactttagtggatagttagctaaatactgattattatgaagtttgcttatctattgttgtctggcag

Basic information

species Zea mays
transcript GRMZM2G039325_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 5'ss of exon 9
TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGTCATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtccatttctttccttattcgttcactttagtggatagttagctaaatactgattattatgaagtttgcttatctattgttgtctggcag
|||||| || ||||||||| |||| || ||||||||||||||||||||| ||||||||||||| ||||||| ||||||||||||||||||||| |||||||||||     ||||   | |||||| |||    | |||  ||||  ||||  |||       |||  || ||| | | | | || |||||   |||
TGGTTTTCTTTATGATATGTTGCAGAAGGAGGTAATTTCTTTGAGAAAGGCATGCCATGAAAAAGATCAGAGTCTAAAAGATAAAGATGATGCGATTGAGgtatggaaatattt---tgcttatttgttgcactgagttcataggaagctcgata-------ttagaaaatttacctgtttcttcttgtcctacag

upper sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 9
TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGTCATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtccatttctttccttat--tcgttcactttagtggatagttagc---taaatactgattattatgaagtttgcttatctattgttgtctggcag
  || |  |||||||  | |||||||||||||| ||  | ||||| ||  |  | || || || ||||| |  |||||||||||||||||||||||||||||| | ||    |   ||  || |  | |   |   |  | ||    |      |||||  |  |  ||   || | |    |    |  |  |||  |||
CAGTGTTTTATATGACTTTCTGCAAAAAGAGGTCATAGCCTTGAGGAAAGCTGGTCACGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCTATTGAGgtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcag

upper sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGTCATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtccatttctttccttattcgttcactttagtggatagttagctaaatactgattattatgaagtttgcttatctattgttgtctggcag
 ||  |  |||||||||||||||||||||||||  |||||||||| ||  |  | |||||||| ||||| |  || |||||||| |||||||||||||||||  |     |||  | |||| ||  ||    |      |||  ||   |  ||| |  |  | ||| | ||||  | |  ||| || |   |   
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggt----attcttgtcctcatctgtcttat------gatgctttaattcatatttttgctcatgta-tttggatgta-attctttttcag---

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|16926574|gb|BM079642.1|BM079642
EST:     CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
genomic: CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
EST: gi|16378770|gb|BI992594.1|BI992594
EST:     CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
genomic: CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
EST: gi|14202547|gb|BG836224.1|BG836224
EST:     CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
genomic: CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
EST: gi|6012204|gb|AW061746.1|AW061746
EST:     CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
genomic: CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
EST: gi|29945923|gb|CB815888.1|CB815888
EST:     CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
genomic: CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
EST: gi|71760015|gb|DR957952.1|DR957952
EST:     CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
genomic: CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
EST: gi|211530545|gb|FL066727.1|FL066727
EST:     CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
genomic: CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
EST: gi|14202541|gb|BG836218.1|BG836218
EST:     CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
genomic: CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
EST: gi|78024888|gb|DV493275.1|DV493275
EST:     AAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
genomic: AAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
EST: gi|78024574|gb|DV492961.1|DV492961
EST:     CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
genomic: CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
EST: gi|148967768|gb|EE019045.2|EE019045
EST:     CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAG                         ATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT
genomic: CATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCT

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: 565

TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGTCATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCTAGAAAGGTCAGACGAGAGGTTGCAGCCATGGAGAAAGAAGTTGCAGCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 181

TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGTCATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCTAGAAAGGTCAGACGAGAGGTTGCAGCCATGGAGAAAGAAGTTGCAGCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 109

TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGTCATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCTAGAAAGGTCAGACGAGAGGTTGCAGCCATGGAGAAAGAAGTTGCAGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGTCATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtcc ... tgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCTAGAAAGGTCAGACGAGAGGTTGCAGCCATGGAGAAAGAAGTTGCAGCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGTCATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtccatttctttccttattcgttcactttagtggatagttagctaaatactgattattatgaagtttgcttatctattgttgtctggcag

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