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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAACCTCGGCGAGATGATGACGCTCGGTAGAAATGATGCCGCGGTAACAGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacacttggtgcacgctcctcgacttccgcgcgcgtatttgtagctgaaattgaacttggctctgcag

Basic information

species Zea mays
transcript GRMZM2G080044_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080044_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g11140.1 (Oryza sativa), 5'ss of exon 10
CAGAACCTCGGCGAGATGATGACGCTCGGTAGAAATGATGCCGCGGTAACAGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacacttggtg-cacgctcct---cgacttccgcgcg----cgtatttgtagctgaaattgaacttggctctgcag
|| || || || ||||||||||| || ||||||| |||||| ||| |||||||||| || ||||| || |||||||||||||||||| | || ||||| |||| |||  ||    | || | || |   |   ||  ||           |||     | | ||| ||||||| |||||||
CAAAATCTTGGTGAGATGATGACACTTGGTAGAAGTGATGCTGCGATAACAGCAAGCTTTATTGAGGGCCTGACCTTGGAAGGACCTTTAGGGCATGCTGgtatgaatcctcaccggcatgttcttttcctgtttttgcataattttacgtttaagaataacattcaacttggttctgcag
















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|5607999|gb|AI901666.1|AI901666
EST:     AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCTG                         CTCGGAAGCTCGTGTACTGCCTCAGAATGCCCNCGGATGAGCCCCGGGTGA
genomic: AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacac ... ggctctgcagCTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGA
EST: gi|29544145|gb|CB604525.1|CB604525
EST:     AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCG                         CTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGA
genomic: AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacac ... ggctctgcagCTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGA
EST: gi|31405661|gb|CD484393.1|CD484393
EST:     AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCG                         CTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGA
genomic: AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacac ... ggctctgcagCTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGA
EST: gi|78025942|gb|DV494329.1|DV494329
EST:     AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCTG                         CTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGA
genomic: AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacac ... ggctctgcagCTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGA
EST: gi|31910982|gb|CD651696.1|CD651696
EST:     AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCG                         CTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGAGAGA
genomic: AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacac ... ggctctgcagCTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGA
EST: gi|78027652|gb|DV496039.1|DV496039
EST:     AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCTG                         CTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGA
genomic: AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacac ... ggctctgcagCTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGA
EST: gi|30306788|gb|CD001461.1|CD001461
EST:     AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCG                         CTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGA
genomic: AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacac ... ggctctgcagCTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGA
EST: gi|211318170|gb|FL216128.1|FL216128
EST:     AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCG                         CTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGA
genomic: AGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacac ... ggctctgcagCTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGA

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: 44 (upstream exon), 42 (downstream exon)
Score: 40

CAGAACCTCGGCGAGATGATGACGCTCGGTAGAAATGATGCCGCGGTAACAGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacac ... ggctctgcagCTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGAAGGTTGGGATCAGCTGGTTCACAAAGGCTGCGATCGATTCGCTTGCCTC


Block sizes: 36 (upstream exon), 42 (downstream exon)
Score: 15

CAGAACCTCGGCGAGATGATGACGCTCGGTAGAAATGATGCCGCGGTAACAGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacac ... ggctctgcagCTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGAAGGTTGGGATCAGCTGGTTCACAAAGGCTGCGATCGATTCGCTTGCCTC


Block sizes: 29 (upstream exon), 36 (downstream exon)
Score: 4

CAGAACCTCGGCGAGATGATGACGCTCGGTAGAAATGATGCCGCGGTAACAGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacac ... ggctctgcagCTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGAAGGTTGGGATCAGCTGGTTCACAAAGGCTGCGATCGATTCGCTTGCCTC


Block sizes: 37 (upstream exon), 33 (downstream exon)
Score: 19

CAGAACCTCGGCGAGATGATGACGCTCGGTAGAAATGATGCCGCGGTAACAGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacac ... ggctctgcagCTCGGAAGCTCGTGTACTGCCTCAGAATGCCCACGGATGAGCACCGGGTGAAGGTTGGGATCAGCTGGTTCACAAAGGCTGCGATCGATTCGCTTGCCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAACCTCGGCGAGATGATGACGCTCGGTAGAAATGATGCCGCGGTAACAGCAAGTTTCATTGAAGGGCTGACCTTGGAAGGACCTCTCGGACATGCCGgtacgaacacttggtgcacgctcctcgacttccgcgcgcgtatttgtagctgaaattgaacttggctctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG