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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCTGCAAGCCACTGTGAGGAAGCAACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcatctgctgggctcttttctgtcttcaaacctggattgtaatgtggctatactgttcatctcaccgtactgtccatgcag

Basic information

species Zea mays
transcript GRMZM2G010834_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010834_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os08g25310.1 (Oryza sativa), 5'ss of exon 14
GTGCTGCAAGCCACTGTGAGGAAGCAACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcatctgctgggctcttttctgtcttcaaacctggattgtaatgtggc-tatactgttcatctcaccgtactg-tccatgcag-------------
||||||||||| || |||| ||||||||||||||  || || ||  ||||||||||||||||       |||   |||| ||     |||    ||| ||   ||||| ||| |||||||   | |    |  |   | |||||||| ||  |  | |||  |              
GTGCTGCAAGCTACCGTGATGAAGCAACTGGAAATTGCAGAATCAATAGAGGAAGTGATTAGGAGGCAGCTAAGGgtaaaattggtcgctcc-ttctgtttcatcttctaacatggattggcgtatcatatgcatattccatctcactgttttcctgcattgactctccttacacag
















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|8383310|gb|BE056253.1|BE056253
EST:     AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCT                         AGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
genomic: AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
EST: gi|18053150|gb|BM318808.1|BM318808
EST:     AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCT                         AGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
genomic: AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
EST: gi|71417469|gb|DR804067.1|DR804067
EST:     AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCT                         AGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
genomic: AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
EST: gi|29945067|gb|CB815452.1|CB815452
EST:     AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCT                         AGACGAAGATTTTGTTTATAACA-GGAACCAGTACTGCTGAAATCAAGATA
genomic: AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
EST: gi|88758386|gb|DY542755.1|DY542755
EST:     AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCT                         AGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
genomic: AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
EST: gi|78180656|gb|DV550984.1|DV550984
EST:     AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCT                         AGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
genomic: AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
EST: gi|50332897|gb|CO528023.1|CO528023
EST:     AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCT                         AGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
genomic: AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
EST: gi|8577208|gb|BE129845.1|BE129845
EST:     AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCT                         AGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
genomic: AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
EST: gi|50332896|gb|CO528022.1|CO528022
EST:     AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCT                         AGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
genomic: AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
EST: gi|4681263|gb|AI629933.1|AI629933
EST:     AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCT                         AGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
genomic: AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
EST: gi|22489115|gb|BU049038.1|BU049038
EST:     AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCT                         AGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
genomic: AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
EST: gi|60398258|gb|DN231074.1|DN231074
EST:     AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCT                         AGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA
genomic: AACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATA

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), 48 (downstream exon)
Score: 25

GTGCTGCAAGCCACTGTGAGGAAGCAACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATACATCCTGTCGCGGAGAAAAATATGCACAGGAATTCGATTGGTGATGTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 115

GTGCTGCAAGCCACTGTGAGGAAGCAACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATACATCCTGTCGCGGAGAAAAATATGCACAGGAATTCGATTGGTGATGTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 202

GTGCTGCAAGCCACTGTGAGGAAGCAACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATACATCCTGTCGCGGAGAAAAATATGCACAGGAATTCGATTGGTGATGTGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 137

GTGCTGCAAGCCACTGTGAGGAAGCAACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcat ... gtccatgcagAGACGAAGATTTTGTTTATAACAAGGAACCAGTACTGCTGAAATCAAGATACATCCTGTCGCGGAGAAAAATATGCACAGGAATTCGATTGGTGATGTGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCTGCAAGCCACTGTGAGGAAGCAACTGGAAAGCGCTGAGTCCCTAGAGGAAGTGATTAGATCAAGCCTACCTgtaagatcatctgctgggctcttttctgtcttcaaacctggattgtaatgtggctatactgttcatctcaccgtactgtccatgcag

- - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA