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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaatttgtccaaatttccatatgccatacataatcatgttatgcctgggagttctcttctcatcgttcacatcttttcactgtttctcttgatactagGTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTGTCATGCG

Basic information

species Oryza sativa
transcript LOC_Os07g39010.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g39010.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G060762_T01 (Zea mays), 3'ss of exon 11
ttaaatttgtccaaatttc-catatgcca-tacataatcatgttatgcctgggagttctcttctcatcgttcacatcttttcactgtttctcttgatactagGTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTGTCATGCG
| |  |   |   | || | |||||   | |  ||  || ||| ||||   ||   || |||   ||  ||   ||||||    || ||   ||||||| |||| |||||||| |||||||||||  |||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |
tcagctgaatttcatttacacatattttagtgtatgctcttgtgatgcaatgggagtcacttag-ataattt-tatctttcttgtgctttcgttgataccagGTGACAAGTATTAGCATGGAAGGTGTTTTAGTAGGAGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTTTCATGTG

upper sequence: LOC_Os07g39010.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G121458_T01 (Zea mays), 3'ss of exon 11
ttaaatttgtccaaatttccatatgccatacataatcatgttatgcctgggagttctctt---ctcatcgttcacatcttttcactgtttctcttgatactagGTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTGTCATGCG
 | |   |||  || ||| ||  ||   | |||   ||  | ||    | |  |  | ||     | |  | |  |||||| |  || ||   ||||||| |||| |||||||| |||||||||||  || ||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |
-ttatcctgtttaa-ttttcagctgaatttcatttgcacat-atttaagtgtatcttgttaggtacgtaatgcttatctttcctgtgctttggttgataccagGTGACAAGTATTAGCATGGAAGGTGTTCTAGTAGGAGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTTTCATGTG
















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|29638656|gb|CB643665.1|CB643665
EST:     TCATGTATGCACTATCAATCACAATAGGAGTTGCCAATGCTCTTATGACA                         GTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGT
genomic: TCATGTATGCACTATCAATCACAATAGGAGTTGCCAATGCTCTTATGACAgtaagttgtt ... ttgatactagGTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGT
EST: gi|29666892|gb|CB663167.1|CB663167
EST:     TCATGTATGCACTATCAATCACAATAGGAGTTGCCAATGCTCTTATGACA                         GTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGT
genomic: TCATGTATGCACTATCAATCACAATAGGAGTTGCCAATGCTCTTATGACAgtaagttgtt ... ttgatactagGTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGT
EST: gi|29655797|gb|CB652072.1|CB652072
EST:     TCATGTATGCACTATCAATCACAATAGGAGTTGCCAATGCTCTTATGACA                         GTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGT
genomic: TCATGTATGCACTATCAATCACAATAGGAGTTGCCAATGCTCTTATGACAgtaagttgtt ... ttgatactagGTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGT
EST: gi|29630236|gb|CB635245.1|CB635245
EST:     TCATGTATGCACTATCAATCACAATAGGAGTTGCCAATGCTCTTATGACA                         GTAACAAGTATCAGCATGAAAGGAATTTTAGTAGGTGAAGATCTAAATGGT
genomic: TCATGTATGCACTATCAATCACAATAGGAGTTGCCAATGCTCTTATGACAgtaagttgtt ... ttgatactagGTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGT
EST: gi|29666893|gb|CB663168.1|CB663168
EST:     TATGCACTATCAATCACAATAGGAGTTGCCAATGCTCTTATGACA                         GTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGT
genomic: TATGCACTATCAATCACAATAGGAGTTGCCAATGCTCTTATGACAgtaagttgtt ... ttgatactagGTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGT
EST: gi|29630208|gb|CB635217.1|CB635217
EST:     TCATGTATGCACTATCAATCACAATAGGAGTTGCCAATGCTCTTATGACA                         GTAACAAGTATCAGCATGAAAGGAATTTTAGTAGGTGAAGATCTAAATGGT
genomic: TCATGTATGCACTATCAATCACAATAGGAGTTGCCAATGCTCTTATGACAgtaagttgtt ... ttgatactagGTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGT

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: 59 (upstream exon), 52 (downstream exon)
Score: 7

GATATTGTCTGGTGTTGGAATTGTTGTTCTACCAAGTGGAATGCACAACTTCATGTATGCACTATCAATCACAATAGGAGTTGCCAATGCTCTTATGACAgtaagttgtt ... ttgatactagGTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTGTCATGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgggagttctcttctcatcgttcacatcttttcactgtttctcttgatactagGTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTGTCATGCG
                                           tcttgat  putative branch site (score: 7)
                          catcttttcactgttt  CT-rich tract
                           atctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaatttgtccaaatttccatatgccatacataatcatgttatgcctgggagttctcttctcatcgttcacatcttttcactgtttctcttgatactagGTAACAAGTATCAGCATGGAAGGAATTTTAGTAGGTGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTGTCATGCG

- - - - - - - - - -catatgc
- - - - - - - - - - - - - catacat
- - - - - - - - - - - - - - - - - atcatgt
- - - - - - - - - - - - - - - - - - - - - atgcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttct