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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaaatgcttatctggtggcttgactattgaaatcataacatatggttcttactgctgctttttttacgtcaaacatgacatggctctcattttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTGGGCATCGGGCTATTATTCACAGCCATTGCTGCTACATATGTAACACGAC

Basic information

species Oryza sativa
transcript LOC_Os01g66170.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g66170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G068271_T01 (Zea mays), 3'ss of exon 6
-ttgaaatgcttatctggtggcttgactattgaaatcataacatatggttct-tactgctgctttttttacgtcaaacatgacatggctctcattttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTGGGCATCGGGCTATTATTCACAGCCATTGCTGCTACATATGTAACACGAC
 ||| |    || | |  |   | |      |            | |    | ||   | |       |   ||||  |         ||| ||||||||||||||||||||| || || |||||||||||||||   ||||||  |||||||||| | ||  |||| || ||||||||||||||  | ||||||||  | |
cttgtaccattttttttct--ttgggggggggggggggggggggaggacaatgtatgacagacccgaatggatcaatgaaatttgttttcttattttgacagCAAGATGAGTCGGAAATTGGTTTGGGAGGAAACGAACAGCTATGGACACTGGGCGTTGGATTATTGTTTACAGCCATTGCTGCCGCTTATGTAACGAGGC
















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|86496697|gb|CI139330.1|CI139330
EST:     CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATT                         CAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAACCAGCTACTGACACTG
genomic: CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATTgtaagttctt ... attttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
EST: gi|86507543|gb|CI150176.1|CI150176
EST:     CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATT                         CAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
genomic: CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATTgtaagttctt ... attttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
EST: gi|218500098|gb|FG961175.1|FG961175
EST:     ATTTGGACGAGCTATAATT                         CAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
genomic: ATTTGGACGAGCTATAATTgtaagttctt ... attttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
EST: gi|33661898|gb|CF292865.1|CF292865
EST:     CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATT                         CAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
genomic: CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATTgtaagttctt ... attttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
EST: gi|88525273|gb|CI454258.1|CI454258
EST:     CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATT                         CAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
genomic: CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATTgtaagttctt ... attttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
EST: gi|86900089|gb|CI300153.1|CI300153
EST:     CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATT                         CAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
genomic: CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATTgtaagttctt ... attttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
EST: gi|29686432|gb|CB682707.1|CB682707
EST:     CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATT                         CAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
genomic: CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATTgtaagttctt ... attttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
EST: gi|86505655|gb|CI148288.1|CI148288
EST:     CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATT                         CAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
genomic: CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATTgtaagttctt ... attttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
EST: gi|88998330|gb|CI038215.1|CI038215
EST:     CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATT                         CAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
genomic: CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATTgtaagttctt ... attttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
EST: gi|58686934|gb|CK075621.1|CK075621
EST:     CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATT                         CAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
genomic: CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATTgtaagttctt ... attttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
EST: gi|86497649|gb|CI140282.1|CI140282
EST:     CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATT                         CAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
genomic: CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATTgtaagttctt ... attttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
EST: gi|86889147|gb|CI315758.1|CI315758
EST:     CAGGATCATGGCCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATT                         CAAGATGAGTCAGAAATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG
genomic: CAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATTgtaagttctt ... attttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTG

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: 70 (upstream exon), 53 (downstream exon)
Score: 37

TTGGTTGGGAATGCTTCCAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATTgtaagttctt ... attttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTGGGCATCGGGCTATTATTCACAGCCATTGCTGCTACATATGTAACACGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttcttactgctgctttttttacgtcaaacatgacatggctctcattttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTGGGCATCGGGCTATTATTCACAGCCATTGCTGCTACATATGTAACACGAC
  ttcttac  putative branch site (score: 37)
                                        ctctcatttt  putative PPT
               ttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaaatgcttatctggtggcttgactattgaaatcataacatatggttcttactgctgctttttttacgtcaaacatgacatggctctcattttgacagCAAGATGAGTCAGAGATCGGTTTGGGAGGAAACAGCCAGCTACTGACACTGGGCATCGGGCTATTATTCACAGCCATTGCTGCTACATATGTAACACGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - aatgctt
- - - - - - -ctggtgg
- - - - - - - - - - - - - - - - - - - - - - tggttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacatg