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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGTTATCGGCGCCAAGGACCCCACTGAATGATGCACAAAAACGTGCACAGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcacatttattccattttcccttatgtgcatttcaaatgactaaaggatagtgaatgtttgtgtttttagtcagtagtcttgggttccatttct...

Basic information

species Zea mays
transcript GRMZM2G063806_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063806_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os07g26440.1 (Oryza sativa), 5'ss of exon 9
GAGGTTATCGGCGCCAAGGACCCCACTGAATGATGCACAAAAACGTGCACAGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgt-tttttcacatttattccattttcccttatgtgcatttcaaatgactaaaggatagtgaatgtttgtgtttttagt-cagtagtcttgggttccatttct
|||| | || || |||| ||||||||| ||||||||||| ||||||||||||||| |||| |||||||| || || || ||||||||||||||||| ||||| || ||   ||||   || || |    |    ||| ||  ||  ||| |    |  || ||| |     |||  || || ||||      ||   |||  
GAGGCTCTCTGCTCCAAAGACCCCACTCAATGATGCACAGAAACGTGCACAGAACATGCGAGCATATAAAGCTGATCTCCAGAAACTGAAGAAAGAGCAGgtattgtttctattttcccctttcttgtctccaagcagtttgaa--acttagttcttctgcatggtgtaaatttaggtacattagttgacaattttttttaa
















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|18385223|gb|BM418422.1|BM418422
EST:     AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAG                         GAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
genomic: AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
EST: gi|78180272|gb|DV550645.1|DV550645
EST:     AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAG                         GAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
genomic: AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
EST: gi|87152901|gb|DY397690.1|DY397690
EST:     AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAG                         GAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
genomic: AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
EST: gi|113768032|gb|DW884002.1|DW884002
EST:     AGAAACTGAAGAAAGAACAG                         GAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAA
genomic: AGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAA
EST: gi|18172754|gb|BM348142.1|BM348142
EST:     AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAG                         GAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
genomic: AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
EST: gi|40335048|gb|CK369118.1|CK369118
EST:     AGAACCTGCGTGCATATAAGGCAGACCTTCATAAACTGAAGAAAGAACAG                         GAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
genomic: AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
EST: gi|37380223|gb|CF626899.1|CF626899
EST:     AGAACCTGCGTGCATATAAGGCAGACCTTCATAAACTGAAGAAAGAACAG                         GAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
genomic: AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
EST: gi|19821783|gb|BQ047807.1|BQ047807
EST:     AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAG                         GAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
genomic: AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
EST: gi|17970287|gb|BM277050.1|BM277050
EST:     AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAG                         GAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
genomic: AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
EST: gi|60348586|gb|DN215559.1|DN215559
EST:     AGAACCTGCGTGCATACAAGGCAGACCTTCAGAAACTGAAGAAAGAACAG                         GAAGAAGAGCAAATAAAGCGATTGGAGAGGCTC
genomic: AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTC
EST: gi|6742525|gb|AW313340.1|AW313340
EST:     AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAG                         GAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG
genomic: AGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAG

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: 46 (upstream exon), 49 (downstream exon)
Score: 120

GAGGTTATCGGCGCCAAGGACCCCACTGAATGATGCACAAAAACGTGCACAGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAGAGGATCGCCGCAAGAGGTAATGGAAAGGGTCCAGGGAATGGTTCTCCTA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 163

GAGGTTATCGGCGCCAAGGACCCCACTGAATGATGCACAAAAACGTGCACAGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAGAGGATCGCCGCAAGAGGTAATGGAAAGGGTCCAGGGAATGGTTCTCCTA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 109

GAGGTTATCGGCGCCAAGGACCCCACTGAATGATGCACAAAAACGTGCACAGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAGAGGATCGCCGCAAGAGGTAATGGAAAGGGTCCAGGGAATGGTTCTCCTA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 126

GAGGTTATCGGCGCCAAGGACCCCACTGAATGATGCACAAAAACGTGCACAGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcac ... atattttcagGAAGAAGAGCAAATAAAGCGATTGGAGAGGCTCAAATTGGAGCGGCAAAAGAGGATCGCCGCAAGAGGTAATGGAAAGGGTCCAGGGAATGGTTCTCCTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGTTATCGGCGCCAAGGACCCCACTGAATGATGCACAAAAACGTGCACAGAACCTGCGTGCATATAAGGCAGACCTTCAGAAACTGAAGAAAGAACAGgttttttcacatttattccattttcccttatgtgcatttcaaatgactaaaggatagtgaatgtttgtgtttttagtcagtagtcttgggttccatttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaggata