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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTAACCTTATTGGAGGTGATACACTATTTGGCCGGTTATGGGGATGCCTGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgctcatgtttggaaccatagaacaatgccaatatatggtccgcttacagtatagtgatattgtccag

Basic information

species Zea mays
transcript GRMZM2G158097_T03
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158097_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g36062.2 (Oryza sativa), 5'ss of exon 10
TCTTAACCTTATTGGAGGTGATACACTATTTGGCCGGTTATGGGGATGCCTGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgctcatgtttggaacc--atagaacaatgccaatatatggtccgcttacagtata----gtgatattgtccag--------------------
||||||||||||||||||||| ||| | |||||||| |||||||| || |||||||||||||| || |||||||||||||||||||||||||||||||||||| ||||  ||| | |   | |  | ||||      |   |||  |    |||| | |||     |   ||    |                       
TCTTAACCTTATTGGAGGTGACACATTGTTTGGCCGCTTATGGGGCTGTCTGCCAGATGCTTATTTCCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtaatttgtgcatctctcagagcttacagaatgtgaacttcataatggaaacttataatatgtattgcagtagcacctgaatatgtttcaaaaccatttc

upper sequence: GRMZM2G158097_T03 (Zea mays), 5'ss of exon 10
lower sequence: Vv12s0035g01750.t01 (Vitis vinifera), 5'ss of exon 10
TCTTAACCTTATTGGAGGTGATACACTATTTGGCCGGTTATGGGGATGCCTGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtat---tttgctcatgtttggaaccatagaac--aatgccaatatat----ggtccgcttacagtatagtgatattgtccag------------------
||| || ||||||||||| |||||  |||| ||||| ||||||||||| || |||   ||||| | ||| |  |||||||||||||| |||||||| ||||| |   | ||    ||||   | |  || | |  ||  | |   |      || ||  ||| | |  ||  |||||  |  |                  
TCTCAATCTTATTGGAGGAGATACTTTATTCGGCCGCTTATGGGGATGTCTCCCACGAGCTTATTATCCTAGCTTGCATTTTGAAGCATGCTATTACCAGgtttggatctgactttgttctcatcagtaaagctgaactctatggtccaccaggaccatttaaaatg-agaaatattagctggtaacttttttttttttga
















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|71766749|gb|DR964686.1|DR964686
EST:     TTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|71766886|gb|DR964823.1|DR964823
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32841492|gb|CD981173.1|CD981173
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32841296|gb|CD980977.1|CD980977
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32841005|gb|CD980686.1|CD980686
EST:     CATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: CATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|78124181|gb|DV542565.1|DV542565
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32840850|gb|CD980531.1|CD980531
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|71766748|gb|DR964685.1|DR964685
EST:     TTTGAAGCTTGCTATTTTCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGGGGAGGCAGGTGCT
genomic: TTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32841147|gb|CD980828.1|CD980828
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32840869|gb|CD980550.1|CD980550
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32841261|gb|CD980942.1|CD980942
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|13389377|gb|BG462692.1|BG462692
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGA
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGA
EST: gi|32841581|gb|CD981262.1|CD981262
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
EST: gi|32841639|gb|CD981320.1|CD981320
EST:     TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAG                         GCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT
genomic: TGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCT

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), 47 (downstream exon)
Score: 39

TCTTAACCTTATTGGAGGTGATACACTATTTGGCCGGTTATGGGGATGCCTGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCTCAGGGAGAGCACAAGATCCAGCGTGGTTACCTCCCAGTGACAACTTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

TCTTAACCTTATTGGAGGTGATACACTATTTGGCCGGTTATGGGGATGCCTGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCTCAGGGAGAGCACAAGATCCAGCGTGGTTACCTCCCAGTGACAACTTACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 42

TCTTAACCTTATTGGAGGTGATACACTATTTGGCCGGTTATGGGGATGCCTGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCTCAGGGAGAGCACAAGATCCAGCGTGGTTACCTCCCAGTGACAACTTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

TCTTAACCTTATTGGAGGTGATACACTATTTGGCCGGTTATGGGGATGCCTGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgct ... tattgtccagGCAATTGAAGCAGCCATAGAGTTAAACCTGAGTAAGGTGGAGGCAGGTGCTCAGGGAGAGCACAAGATCCAGCGTGGTTACCTCCCAGTGACAACTTACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTAACCTTATTGGAGGTGATACACTATTTGGCCGGTTATGGGGATGCCTGCCAGATGCTTACTTTCCCAATTTGCATTTTGAAGCTTGCTATTATCAGgtattttgctcatgtttggaaccatagaacaatgccaatatatggtccgcttacagtatagtgatattgtccag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC