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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATCGAGTGGAGCCCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCACgtaactcactcactcactctttaccatctcccatgcatgttttagatgtgcactgaaacgtcatgtctagtatttgctgacgcttctcctgaatttggctgggtttag

Basic information

species Zea mays
transcript GRMZM2G458888_T01
intron # 9
splice site 5'
intron type U2

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|211433222|gb|FL465175.1|FL465175
EST:     CCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCAC                         AATCTGGGACCTTTCATTGGAACGGGACACCGAGGAGGAGGCTGAGTTCAG
genomic: CCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCACgtaactcact ... ctgggtttagAATCTGGGACCTTTCATTGGAACGGGACACCGAGGAGGAGGCTGAGTTCAG
EST: gi|37393369|gb|CF633947.1|CF633947
EST:     CCACACGAAGCATCATCATTGGCTGTAACATCTGAAGACCACCTGCTCAC                         AATCTGGGACCTTTCATTGGAACGTGACACCGAGGAGGAGGCTGAGTTCAG
genomic: CCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCACgtaactcact ... ctgggtttagAATCTGGGACCTTTCATTGGAACGGGACACCGAGGAGGAGGCTGAGTTCAG
EST: gi|33092801|gb|CF052795.1|CF052795
EST:     CCACACGAAGTATCATCATTGGCTGTAACATCTGAAGACCACCAGCTCAC                         AATTTTTGACCTTTCATTGGAACGTGACACCGAGGAGGAGGCTGAGTTCAG
genomic: CCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCACgtaactcact ... ctgggtttagAATCTGGGACCTTTCATTGGAACGGGACACCGAGGAGGAGGCTGAGTTCAG
EST: gi|211433223|gb|FL465176.1|FL465176
EST:     CCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCAC                         AATCTGGGACCTTTCATTGGAACGGGACACCGAGGAGGAGGCTGAGTTCAG
genomic: CCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCACgtaactcact ... ctgggtttagAATCTGGGACCTTTCATTGGAACGGGACACCGAGGAGGAGGCTGAGTTCAG
EST: gi|87156090|gb|DY400879.1|DY400879
EST:     CCACACGAAGCATCATCATTGGCTGTAACATCTGAAGACCACCAGCTCAC                         AATCTGGGACCTTTCATTGGAACGTGACACCGAGGAGGAGGCTGAGTTCAG
genomic: CCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCACgtaactcact ... ctgggtttagAATCTGGGACCTTTCATTGGAACGGGACACCGAGGAGGAGGCTGAGTTCAG
EST: gi|26558492|gb|CA830727.1|CA830727
EST:     CCACACGAAGCATCATCATTGGCTGTAACATCTGAAGACCACCAGCTCAC                         AATCTGGGACCTTTCATTGGAACGTGACACCGAGGAGGAGGCTGAGTTCAG
genomic: CCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCACgtaactcact ... ctgggtttagAATCTGGGACCTTTCATTGGAACGGGACACCGAGGAGGAGGCTGAGTTCAG
EST: gi|40336456|gb|CK370526.1|CK370526
EST:     CCACACGAAGCATCATCATTGGCTGTAACATCTGAAGACCACCTGCTCAC                         AATCTGGGACCTTTCATTGGAACGTGACACCGAGGAGGAGGCTGAGTTCAG
genomic: CCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCACgtaactcact ... ctgggtttagAATCTGGGACCTTTCATTGGAACGGGACACCGAGGAGGAGGCTGAGTTCAG
EST: gi|22472647|gb|BU037127.1|BU037127
EST:     CCACACGAAGCATCATCATTGGCTGTAACATCTGAAGACCACCAGCTCAC                         AATCTGGGACCTTTCATTGGAACGTGACACCGAGGAGGAGGCTGAGTTCAG
genomic: CCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCACgtaactcact ... ctgggtttagAATCTGGGACCTTTCATTGGAACGGGACACCGAGGAGGAGGCTGAGTTCAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 52

TAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATCGAGTGGAGCCCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCACgtaactcact ... ctgggtttagAATCTGGGACCTTTCATTGGAACGGGACACCGAGGAGGAGGCTGAGTTCAGAGCGAAGATGAAAGAGCAGGCAAACGCCCCTGACGATTTGCCGCCTCAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 48

TAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATCGAGTGGAGCCCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCACgtaactcact ... ctgggtttagAATCTGGGACCTTTCATTGGAACGGGACACCGAGGAGGAGGCTGAGTTCAGAGCGAAGATGAAAGAGCAGGCAAACGCCCCTGACGATTTGCCGCCTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 64

TAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATCGAGTGGAGCCCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCACgtaactcact ... ctgggtttagAATCTGGGACCTTTCATTGGAACGGGACACCGAGGAGGAGGCTGAGTTCAGAGCGAAGATGAAAGAGCAGGCAAACGCCCCTGACGATTTGCCGCCTCAG


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 53

TAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATCGAGTGGAGCCCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCACgtaactcact ... ctgggtttagAATCTGGGACCTTTCATTGGAACGGGACACCGAGGAGGAGGCTGAGTTCAGAGCGAAGATGAAAGAGCAGGCAAACGCCCCTGACGATTTGCCGCCTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGCACATTTTGAGTACCACAAGAAAGCAATTACATCCATCGAGTGGAGCCCACACGAAGCATCATCATTAGCTGTAACATCTGAAGACCACCAGCTCACgtaactcactcactcactctttaccatctcccatgcatgttttagatgtgcactgaaacgtcatgtctagtatttgctgacgcttctcctgaatttggctgggtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA