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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtgggatggagggagcatttgcattggttatggtgctagtagttttttaatgacataaagaagtttatgtgatataatcttgctcatccttttgttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g62640.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 6
------gagtgggatggagggagcatttgcattggttatggtgctagt-agttttttaatgacataaagaagtttatgtgatataatcttgctcatccttttgttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG
       | | | |  | | | || |||       ||      ||||| ||  || |||  | |||| |   ||  ||   | ||||   | |  || ||||| ||||||||||||| ||||| |||||||| || |||| | ||||||| ||||| ||| ||||||||
tttgtgtaatcgtacag-gcgtgcttttttgaaaattggccacctagtcagacttgtaagtatataatg---ttactgcattttaat---ggttgtcgttttggtagGTGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 6
gagtgggatggagggagcatttgcattggt-tatggtgctagtagttttttaatgacataaagaagtttatgtgatataatcttgctcatccttttgtt--agGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG
  |  | |   ||       || |||   |  ||       | | ||||| ||||    ||| |     | ||    | ||  |     | | ||| ||  |||||||||||||||||| |||||||| |||||||   | ||||| || || ||| | || |||
--gaagaagacagtttatggttacatacatacataaaaactgaactttttcaatgttggaaacagccaca-gtacagttatgatatctgtacgtttatttcagGTGAACAAGGGATGGTTGATGAAGCGCAGAAAGCACTAGAAGAGGCGGAAGCTCTTAAGAAG

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT3G03340.1 (Arabidopsis thaliana), 3'ss of exon 6
gagtgggatggagggagcatttgcattggttatggtgctagtagttttttaatgacataaagaagtttatgtgatataatcttgctcat----ccttttg-----ttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG
           ||| |   | | |      |||| | |||    | | |||| || | |  | | || | |   | | || | | |  |       ||||     |||||||||||||| ||||| |||||||| |||||||   ||||||| || || ||| | || |||
---------taaggaaatttcttcccgttgtatgttactatatctatgttaaggaaacactggacttcacgaagttttatatagattgtatggttatttgatattttagGTGAACAAGGAATGGTTGATGAAGCCCAGAAAGCCCTGGAAGAGGCTGAAGCTCTTAAGAAG

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|29623140|gb|CB628151.1|CB628151
EST:     TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTG                         GTGAACA-GGGATGGTAGATGAAGCACAGAAAG
genomic: TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTGgtatgaaaag ... cttttgttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAG
EST: gi|29623911|gb|CB628922.1|CB628922
EST:     TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGG
genomic: TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTGgtatgaaaag ... cttttgttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGG
EST: gi|29661287|gb|CB657562.1|CB657562
EST:     TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGGATGGTAGATGAAGCACAGAAAG
genomic: TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTGgtatgaaaag ... cttttgttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAG
EST: gi|29630312|gb|CB635321.1|CB635321
EST:     TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGG
genomic: TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTGgtatgaaaag ... cttttgttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGG
EST: gi|29629756|gb|CB634765.1|CB634765
EST:     TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGG
genomic: TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTGgtatgaaaag ... cttttgttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGG
EST: gi|84117476|gb|CD151243.1|CD151243
EST:     TCGCACTCTAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGG
genomic: TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTGgtatgaaaag ... cttttgttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGG
EST: gi|29664072|gb|CB660347.1|CB660347
EST:     TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGGATGGT
genomic: TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTGgtatgaaaag ... cttttgttagGTGAACAAGGGATGGT
EST: gi|29621718|gb|CB626729.1|CB626729
EST:     TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGG
genomic: TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTGgtatgaaaag ... cttttgttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGG
EST: gi|29639321|gb|CB644330.1|CB644330
EST:     TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTG                         GTGAACA-GGGATGGTAGATG
genomic: TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTGgtatgaaaag ... cttttgttagGTGAACAAGGGATGGTAGATG
EST: gi|29674744|gb|CB671019.1|CB671019
EST:     TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGG
genomic: TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTGgtatgaaaag ... cttttgttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGG
EST: gi|29678347|gb|CB674622.1|CB674622
EST:     TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTG                         GTGAACAAGGGATGGTAGAT
genomic: TCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTGgtatgaaaag ... cttttgttagGTGAACAAGGGATGGTAGAT

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 1 RNA-Seqlibrary.


Block sizes: 63 (upstream exon), 64 (downstream exon)
Score: 27

ACTCCAACACCTCAAATGGCATCAGTACCAGCACCTGCTCCCCCTGATGCTCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTGgtatgaaaag ... cttttgttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttaatgacataaagaagtttatgtgatataatcttgctcatccttttgttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG
 ttttaat  putative branch site (score: 27)
                                  tcttgctcatcctttt  putative PPT
                    tttatgtgatataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtgggatggagggagcatttgcattggttatggtgctagtagttttttaatgacataaagaagtttatgtgatataatcttgctcatccttttgttagGTGAACAAGGGATGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- -tgggatg
- - - - - - - - -catttgc
- - - - - - - - - - - - - - - -atggtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - acataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgata