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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAGgtgatcatttcatatgactgatcgcttgccctagaaagtggaactttatgattgtttcatttttttttgtagtgactttttttttggcttccaataatcctctatagttcaaattcgattacttattacacctgttatggcttctcatagttaaccttgaatgttttcatgtattcttctcttgcag

Basic information

species Zea mays
transcript GRMZM2G114337_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114337_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g48700.1 (Oryza sativa), 5'ss of exon 6
TTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAGgtgatcatttcatatgactgatcgctt------gccctagaaagtggaactttatgattgtttcatttttttttgtagtgactttttttttggcttccaataatcctctatagttcaaattcgattacttattacacctgttatggcttctcatagt-taaccttgaatgttttcatgtattcttctcttgcag
|||||| ||||||||||||||||||||||| ||||||||||| |||||| ||||||||||||| |||| |||||||||||| ||||||||||| ||  ||| |||||  | ||   |       |   |  ||| ||   ||||    ||   |  | ||   || ||   |  |||     || | |     | | || ||| | |    |    ||||    | |  || |||    ||  | ||| ||||||   |  || | || | || | |||||||||
TTTTGACGATCCTGGTCCACATGGAGCAGGCAGATATTCTGATCATATGCTACCTGAAATTGTTAAGAGAGATTGGAGAAAAGGTGCACAGgt-atactttaatatgcataatttttctagaaagtattgcaaactgttgctttgccttttcattttcttcccttttacaaatgtttagagcgggtgctgtggaacttcaataatcctgggtattatactctaaagaattgctatattgtcatacagtctaacctcacacattctgatatgttttcctcttgcag

upper sequence: GRMZM2G114337_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv11s0103g00490.t01 (Vitis vinifera), 5'ss of exon 6
TTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAGgtgatcatttcatatga---ctgatcgcttgccctagaaagtggaactttatgattgtttcatttttttttgtagtgactttttttttggct--tccaataatcctctatagttcaaattcgattacttattacacctgttatggcttctcatagttaaccttgaatgttttcatgtattcttctcttgcag
 ||||| ||||||||||||||||||   || |||||||| || ||||||||||| ||||||| || ||  || |  |||||||| |||||||| || || |||| |     | ||   |||||  | |   |||   |  || ||    || || | ||| |||  | |||||  |    | |  |   | |||                                                                                         
CTTTGAGGATCCTGGTCCACATGGAAATGGCAGATATTCAGAACATATGTTACCGGAAATTGAGATGAGTGACTTTAGAAAGGGCGCACAGgt-ataatctcatgtattatcagaggccttgcatttgtttgtgagtcagta-gaaaacttgatgtgtttatgt--tcactttgatgaaagttatttggacaata----------------------------------------------------------------------------------------
















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|78544029|gb|DV621527.1|DV621527
EST:     AGGGTGCACAG                         TGG-TTACCAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCT
genomic: AGGGTGCACAGgtgatcattt ... tctcttgcagTGGTTTA-CAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCT
EST: gi|211112077|gb|FL283002.1|FL283002
EST:     ATTGGAGAAAGGGTGCACAG                         TGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
genomic: ATTGGAGAAAGGGTGCACAGgtgatcattt ... tctcttgcagTGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
EST: gi|22818980|gb|BU499070.1|BU499070
EST:     ACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAG                         TGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
genomic: ACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAGgtgatcattt ... tctcttgcagTGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
EST: gi|71762012|gb|DR959949.1|DR959949
EST:     ACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAG                         TGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
genomic: ACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAGgtgatcattt ... tctcttgcagTGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
EST: gi|71773585|gb|DR971483.1|DR971483
EST:     ACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAG                         TGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
genomic: ACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAGgtgatcattt ... tctcttgcagTGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
EST: gi|20802912|gb|BQ293962.1|BQ293962
EST:     GAAGAAAGATTGGAGAAAGGGTGCACAG                         TGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
genomic: GAAGAAAGATTGGAGAAAGGGTGCACAGgtgatcattt ... tctcttgcagTGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
EST: gi|76284047|gb|DV023615.1|DV023615
EST:     TGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAG                         TGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
genomic: TGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAGgtgatcattt ... tctcttgcagTGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
EST: gi|20506952|gb|BQ279416.1|BQ279416
EST:     CATATGTTACCTGAAATTGTGAAGAATAGTATTGGAGAAAGGGTGCACAG                         TGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
genomic: CATATGTTACCTGAAATTGTGAAGAA-AG-ATTGGAGAAAGGGTGCACAGgtgatcattt ... tctcttgcagTGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
EST: gi|26456599|gb|CA828182.1|CA828182
EST:     CCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACANG                         -GGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCT
genomic: CCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACA-Ggtgatcattt ... tctcttgcagTGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCT
EST: gi|211112078|gb|FL283003.1|FL283003
EST:     ACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAG                         TGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT
genomic: ACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAGgtgatcattt ... tctcttgcagTGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTT

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), 47 (downstream exon)
Score: 108

TTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAGgtgatcattt ... tctcttgcagTGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 45

TTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAGgtgatcattt ... tctcttgcagTGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 58

TTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAGgtgatcattt ... tctcttgcagTGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 25

TTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAGgtgatcattt ... tctcttgcagTGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGATGATCCTGGTCCACATGGAGCAGGTAGATATTCTGACCATATGTTACCTGAAATTGTGAAGAAAGATTGGAGAAAGGGTGCACAGgtgatcatttcatatgactgatcgcttgccctagaaagtggaactttatgattgtttcatttttttttgtagtgactttttttttggcttccaataatcctctatagttcaaattcgattacttattacacctgttatggcttctcatagttaaccttgaatgttttcatgtattcttctcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA