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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatataaattacgaaatgcaggggtctgtacttgagtttttctgagacgcatgttatgctgagttgtcaaagctgcttctctgtgatcttttgtaatttcag

Basic information

species Zea mays
transcript GRMZM5G836628_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836628_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g49040.1 (Oryza sativa), 5'ss of exon 4
TCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatataaattacgaaatgcagg-ggtctgtacttgagtttttctgagacgcatgttatgctgagttgt----caaagctgcttctctgtgatcttttgtaatttcag
||||||||||||||| |||||| ||||||| |||||||| ||||||||||||||||| || |||||||||||||| ||||||||||| |||||||| |||||  | ||   ||||  || || | |   | | ||  |   |||||||  |  | ||  ||   | | || |    ||| | ||   || | | |   |  |||||| |||
TCTCCGGTGCTGGCCAGGTGGCCTGTGCCTTTCAAGATCTATCGGGGACATGGATGTCGGGGAGTTCATTGTGCCGATTCCACATGTGAAGCAAGTGAAGgt-gggtagctattagaaagtggatgcaatttctagcttc-tttttctatggtgtattgtagtataatttctttttcaaggttgtcactttcttac--tcggtaattgcag

upper sequence: GRMZM5G836628_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G29060.1 (Glycine max), 5'ss of exon 5
TCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagata--taaattacgaaatgcaggggtctgtact--tgagtttttctgagacgcatgttatgctgagttgtcaaagctgcttctctgtgatcttttgtaatttcag
||| || || ||||||||||| |||||||| || ||||| || || ||||  || || ||||| || ||||| || || ||||||||||||||||| ||||| || ||  |  |||  | | |    |  | |  |    ||    ||     || |  | |  | || | || |||   || ||   || |    | |||      |||
TCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACAGACGTGGGAGAATTTATTGTCCCAATACCACATGTCAAGCAAGTGAAGgtaagctagtttcattttgtagtcttagtttattgatcgatggccattatgtggaagtgtttagtactaaatt-tcagcactcctgacct-tctcttattggttccccag

upper sequence: GRMZM5G836628_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G38270.1 (Glycine max), 5'ss of exon 5
TCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagata--taaattacgaaatgcaggggtctgtacttgag----tttttctg-agacgcatgttatgctgagttgtcaaagctgcttctctgtgatcttttgtaatttcag
||| || |||||||||||||| |||||||| || ||||| || || |||| ||| || ||||| || |||||||| || |||||||| |||||||| ||||| || ||  |  |||  ||| |    |  | | || |   |    ||||| ||  ||    | |  | || | || |||   ||| |   || |    | |||      |||
TCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGCAAGTGAAGgtaagctagtttcattttgaagtcttagtttatatattgatggtcatttttatgtggagatgtttagtactaaatt-tcagcactgatgacct-tctcttattggttccccag

upper sequence: GRMZM5G836628_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv14s0060g01580.t01 (Vitis vinifera), 5'ss of exon 5
TCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgt-tagatataa-attacgaaatgcaggggtctgtacttgagtttttctgagacgc-atgttatgctga-gttgtcaaagctgcttctctgtgatcttttgtaatttcag----------------------
 ||||| |||||||||||||| || || ||||| || || || || ||||  ||||| ||||| |||||||| || || |||||||| |||||||| ||||| |    |    |||  | | ||  |  |  | || |  | || |  |    | | || || | |||  | | |      | |||     || |   || ||| ||||                       
ACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGCAAGTGAAGgtgtgtgcaccttattttgtactggtgatggttttattgcatttgtggtagtccaccatattgtactggtgatatttttattactttctgatggtacattctaagttcaatctcttttaattgattattaag

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|32788846|gb|CD941082.1|CD941082
EST:     TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAG                         CTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGAC
genomic: TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGAC
EST: gi|93012388|gb|EB637908.1|EB637908
EST:     TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAGGTCAAG                         CTATCAAACACCGGAGGAAGACTGATAATAGCATCTG
genomic: TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGATAATAGCATCTG
EST: gi|148932058|gb|EC875401.2|EC875401
EST:     TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAG                         CTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGAC
genomic: TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGAC
EST: gi|71430183|gb|DR811233.1|DR811233
EST:     TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAG                         CTATCAAACACGGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGAC
genomic: TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGAC
EST: gi|149109561|gb|EE190266.2|EE190266
EST:     TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAG                         CTATCAAACACCGGAGGAAGACTGANTA-TAGCATCTGATGGCATATGGGA
genomic: TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGA-TAATAGCATCTGATGGCATATGGGA
EST: gi|148967746|gb|EE019020.2|EE019020
EST:     TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAG                         CTATCAAACACCGGAGGAAGACTGATA
genomic: TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGATA
EST: gi|91050128|gb|EB160546.1|EB160546
EST:     GGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTNCA-GCAAGTCAAG                         CTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGAC
genomic: GGATGTTGGAGAGTTCATTGTGCCCATTCCACATGT-CAAGCAAGTCAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGAC
EST: gi|148958254|gb|EC904468.2|EC904468
EST:     TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAG                         CTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGAC
genomic: TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGAC
EST: gi|149014901|gb|EE044621.2|EE044621
EST:     TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAG                         CTATCAAACCCCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGAC
genomic: TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGAC
EST: gi|78110646|gb|DV529051.1|DV529051
EST:     TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAG                         CTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGAC
genomic: TGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGAC
EST: gi|149101969|gb|EE287481.2|EE287481
EST:     GGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTNCA-G                         CTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGA
genomic: GGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGT-CAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGA

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: 117

TCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGACGCGTTGTCCAATGAAGCAGCTGCAAAAGCATGCAGAGGATTGCCTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

TCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGACGCGTTGTCCAATGAAGCAGCTGCAAAAGCATGCAGAGGATTGCCTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

TCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGACGCGTTGTCCAATGAAGCAGCTGCAAAAGCATGCAGAGGATTGCCTGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 90

TCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatata ... gtaatttcagCTATCAAACACCGGAGGAAGACTGATAATAGCATCTGATGGCATATGGGACGCGTTGTCCAATGAAGCAGCTGCAAAAGCATGCAGAGGATTGCCTGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGCAAGTCAAGgttagatataaattacgaaatgcaggggtctgtacttgagtttttctgagacgcatgttatgctgagttgtcaaagctgcttctctgtgatcttttgtaatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG