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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagcctgttgattaaataatggaaagctgtataagctttcctgcttttagcatgtactagtgcgagccttcatatatatatttatttgccttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGCAGTGAAACCCCTCATACACCAGAGGGAGGAAATGGCAGTGCAGTATGCT

Basic information

species Zea mays
transcript AC148167.6_FGT001
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC148167.6_FGT001 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g08790.1 (Oryza sativa), 3'ss of exon 6
-----ttagc--ctgttgattaaataatggaaagc-tgta-taagctttcctgcttttagcatgtactagtgcgagccttcatatatatatttatttgccttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGCAGTGAAACCCCTCATACACCAGAGGGAGGAAATGGCAGTGCAGTATGCT
      | ||  |  || | |    ||     ||  |||  ||| ||| || ||||||||||||| | | ||   |  ||||        ||| | |    ||| | |||||||||||||||||||||| |||||||||||||||||||||||||||||||| || ||||||||||||||||||||   |||||| ||||||| ||| |
ttcaactggcgaccattaacttgccaacttttagtatgtgctaaacttgccagcttttagcatgtgc-aatgttggtattcac-------tttgtcttttatttat-agGTGCCTCCAACTCGTGCCAAATCACCAAAATTGACACGGAGAAAGAGCTGCAGCGATACCCCTCATACACCAGAGGGTAAAAATGGAAGTGCAGCATGTT
















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|149082929|gb|EE172163.2|EE172163
EST:     TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|22472750|gb|BU037230.1|BU037230
EST:     TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         G-GCCTCCAACTCGTGCCAAG-CACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|21626294|gb|BQ621215.1|BQ621215
EST:     TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|149097421|gb|EE183277.2|EE183277
EST:     TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|149099640|gb|EE185685.2|EE185685
EST:     TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|18168899|gb|BM338739.1|BM338739
EST:     TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|32870635|gb|CF010317.1|CF010317
EST:     GAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: GAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|26457346|gb|CA828929.1|CA828929
EST:     TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|6021796|gb|AW066724.1|AW066724
EST:     AAGG-TGAAC-TAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCANAATTGACACGGAGAAAGAGCTGC
genomic: AAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|78545100|gb|DV622598.1|DV622598
EST:     TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|22472914|gb|BU037394.1|BU037394
EST:     TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|28931378|gb|CB334739.1|CB334739
EST:     TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|21481148|gb|BQ577831.1|BQ577831
EST:     TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|60396357|gb|DN229226.1|DN229226
EST:     CAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: CAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|37386546|gb|CF630460.1|CF630460
EST:     TGCCAAGC-TCTACCAAGAGGGACCCCCACCAAAGG-TGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAA-TGNACACGGAGAAAGAGCTG
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTG-ACACGGAGAAAGAGCTG
EST: gi|22545951|gb|BU098310.1|BU098310
EST:     TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|22819470|gb|BU499560.1|BU499560
EST:     TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|78023911|gb|DV492298.1|DV492298
EST:     TGCCAAGCTT-TACCAAGAGGGACCCCCACCAAAGG-TGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
EST: gi|22472889|gb|BU037369.1|BU037369
EST:     TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAG                         GTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGC

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: 49 (upstream exon), 49 (downstream exon)
Score: 174

AGAAGCTCTAAGACAACTGAGGAAGAACTTGGTCGTCCGAGCAAAACCCATGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGCAGTGAAACCCCTCATACACCAGAGGGAGGAAATGGCAGTGCAGTATGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 87

AGAAGCTCTAAGACAACTGAGGAAGAACTTGGTCGTCCGAGCAAAACCCATGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGCAGTGAAACCCCTCATACACCAGAGGGAGGAAATGGCAGTGCAGTATGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 187

AGAAGCTCTAAGACAACTGAGGAAGAACTTGGTCGTCCGAGCAAAACCCATGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGCAGTGAAACCCCTCATACACCAGAGGGAGGAAATGGCAGTGCAGTATGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 302

AGAAGCTCTAAGACAACTGAGGAAGAACTTGGTCGTCCGAGCAAAACCCATGCCAAGCTTCTACCAAGAGGGACCCCCACCAAAGGTTGAACTTAAGAAGgtaatgtatt ... cttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGCAGTGAAACCCCTCATACACCAGAGGGAGGAAATGGCAGTGCAGTATGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttagcatgtactagtgcgagccttcatatatatatttatttgccttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGCAGTGAAACCCCTCATACACCAGAGGGAGGAAATGGCAGTGCAGTATGCT
                                    tttatttgcctttt  CT-rich tract
                           atatatatatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagcctgttgattaaataatggaaagctgtataagctttcctgcttttagcatgtactagtgcgagccttcatatatatatttatttgccttttgtcagGTGCCTCCAACTCGTGCCAAGTCACCAAAATTGACACGGAGAAAGAGCTGCAGTGAAACCCCTCATACACCAGAGGGAGGAAATGGCAGTGCAGTATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - cctgttg
- - - - - - - - - - - - -agctgta
- - - - - - - - - - - - - - - - - - - - - - - - - gcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccttca