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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaacctgaaaataaaaaccgctccagctgaccacttcatcaaaggaaatatgttgctcctctaaacattattcttcattaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTACACAACAAACTCTGAGGGGTTGGTCATCCACGATGGCACATGGACGTACA

Basic information

species Zea mays
transcript GRMZM2G141473_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141473_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g57680.1 (Oryza sativa), 3'ss of exon 8
-----------------gtcaacctgaaaataaaaaccgctccagc-----------tgaccacttcatcaaaggaa------atatgttgc---tcctctaaac-----attattcttcattaaca-cagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTACACAACAAACTCTGAGGGGTTGGTCATCCACGATGGCACATGGACGTACA
                  | | | | ||||||  |   ||  | ||           |  | |  ||||   | |||       ||  ||     |  ||| ||      ||  || ||  ||   | |||||||||||||||||| | |||||  | |||||||| || |||||||||||||| || ||||| || ||| |||||||| |||| ||||| ||||||||||
gtcagtcaatctactaaattaccttcaaaatatcagttgcatctgcaattctgcgcgttgcaaaatcattgcaagaatgagatgtaaattatatgtgatctgaatgtgcaatcgttgttttttgtgatcagGTGGAAGGCGCATTCGTGCAAGGGATCGGCTTCTTCACGAACGAGGAGTACACGACCAACTCCGATGGGCTGGTCATCAACGACGGCACGTGGACGTACA

upper sequence: GRMZM2G141473_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 8
--------------gtcaacctgaaaataaaaaccgctccagctgaccacttcatcaaaggaaatatgttgctcctctaaacattattcttcattaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTACACAACAAACTCTGAGGGGTTGGTCATCCACGATGGCACATGGACGTACA
               || |  || ||||| | |  |    | ||||   |   ||     |    || ||| |  | |   |  | | | ||  |||  |||||||||||||| ||| | ||||| || |||||||| || |||||||||||| | || ||| | || ||| ||||||||||||| ||||||||||||||||
gcaagaccaatgaaatccatgtgtaaatatatat-gtataatctgaatgcaagattgttagctgaatattgttgattttggcggtctccatcgataat-cagGTGGAAGGCGCGTTCGTGCAAGGTGTGGGCTTCTTCACGAACGAGGAGTACGCGACCAACGCCGATGGGCTGGTCATCCACGACGGCACATGGACGTACA

upper sequence: GRMZM2G141473_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g57720.1 (Oryza sativa), 3'ss of exon 1
gtcaacctgaaaataaaaaccgctccagctgaccacttcatcaaaggaaatatgttgctcctctaaacattattcttcattaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTACACAACAAACTCTGAGGGGTTGGTCATCCACGATGGCACATGGACGTACA
                                        | | |  ||||||||   |   || ||  || ||  || ||     ||||||||||||||||| | |||||  | |||||||| || |||||||||||| | || ||||| || ||| |||||||||||||  |||| ||||||||||
---------------------------------------gtaatactaaatatgta--taaactgaatgttgttgatc-ttggt-tagGTGGAAGGCGCATTCGTGCAAGGGATCGGCTTCTTCACGAACGAGGAGTACGCGACCAACTCCGATGGGCTGGTCATCCACGACAGCACGTGGACGTACA

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|87153969|gb|DY398758.1|DY398758
EST:     GATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTT-GGCCAAG                         GTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTA
genomic: GATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCC-AGgtcaacctga ... attaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTA
EST: gi|5361195|gb|AI795615.1|AI795615
EST:     TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG                         GTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
genomic: TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAGgtcaacctga ... attaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
EST: gi|17921843|gb|BM259479.1|BM259479
EST:     TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG                         GTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
genomic: TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAGgtcaacctga ... attaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
EST: gi|32793565|gb|CD945801.1|CD945801
EST:     TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG                         GTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
genomic: TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAGgtcaacctga ... attaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
EST: gi|17921516|gb|BM259167.1|BM259167
EST:     TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG                         GTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
genomic: TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAGgtcaacctga ... attaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
EST: gi|88758370|gb|DY542739.1|DY542739
EST:     GACTTGGGCCAG                         GTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
genomic: GACTTGGGCCAGgtcaacctga ... attaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
EST: gi|5005980|gb|AI712042.1|AI712042
EST:     TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG                         GTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
genomic: TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAGgtcaacctga ... attaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
EST: gi|5871449|gb|AW017920.1|AW017920
EST:     TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG                         GTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
genomic: TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAGgtcaacctga ... attaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
EST: gi|17921574|gb|BM259225.1|BM259225
EST:     TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG                         GTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
genomic: TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAGgtcaacctga ... attaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
EST: gi|5895925|gb|AW037171.1|AW037171
EST:     TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG                         GTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC
genomic: TTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAGgtcaacctga ... attaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTAC

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: 39 (upstream exon), 31 (downstream exon)
Score: 8

GTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAGgtcaacctga ... attaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTACACAACAAACTCTGAGGGGTTGGTCATCCACGATGGCACATGGACGTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 680

GTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAGgtcaacctga ... attaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTACACAACAAACTCTGAGGGGTTGGTCATCCACGATGGCACATGGACGTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 696

GTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAGgtcaacctga ... attaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTACACAACAAACTCTGAGGGGTTGGTCATCCACGATGGCACATGGACGTACA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 39

GTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAGgtcaacctga ... attaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTACACAACAAACTCTGAGGGGTTGGTCATCCACGATGGCACATGGACGTACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttcatcaaaggaaatatgttgctcctctaaacattattcttcattaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTACACAACAAACTCTGAGGGGTTGGTCATCCACGATGGCACATGGACGTACA
                                            cattaac  putative branch site (score: 39)
                                       ttcttcatt  CT-rich tract
                                   attattcttcattaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaacctgaaaataaaaaccgctccagctgaccacttcatcaaaggaaatatgttgctcctctaaacattattcttcattaacacagGTGGAAGGCGCATTCATCCAAGGAGTAGGCTTCTTTACAAACGAGGAGTACACAACAAACTCTGAGGGGTTGGTCATCCACGATGGCACATGGACGTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA