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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttccttttgcaaaatatactgtacagtatagatatgcaactagacatctatttttaacaacatgccatcactgttttcttattactatatatcaatatcttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCAC

Basic information

species Oryza sativa
transcript LOC_Os08g42410.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G043198_T02 (Zea mays), 3'ss of exon 10
gtagtttccttttgcaaaatatactgtacagtatagatatgcaactagacatctatttttaacaacatgccatcactgttttcttattactatatatcaatatcttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCAC
||| |||  ||||   |  | | ||  ||   |    | |||    |||  || |||||       |  |||     ||| |||||||  |   ||  ||| ||| |  |||||| ||||||||||| |||||||| ||  |||||||||||||||| |||||||| || ||||||||||| |||||||||||| | |||||||| || || |
gtaatttgtttttt--atttcttctaaactacagccttgtgctgtcagatctc-attttccctgggagtcca--gtcgttgtcttattctt---tagtaat-tctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCATCTGTGAGGAAAACCAATAGATTGGTAACCGTAGAAGAAGGCTTCCCTC

upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 3'ss of exon 12
-----------------gtagtttccttttgcaaaatatactgtacagtatagatatgcaactagacatctatttttaacaacatgccatcactgttttcttattactatatatcaatatcttttat-cagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCAC
                 | | |     ||  ||   | |  ||| || | |   |  |    ||||  |  |     |     ||       ||  |||   || | ||   |    | |  | ||  ||| | || ||||| || |||||||||||  |||| | | | || |||||||| ||||| |||||||| |||||| | |||||| |||||||||| || || |
gtaaattaatacttaaagaactcagaattcccatgttttcttgtgcattttcttttgggggttagatttgaaagcaaacagttataatccttctagtttgaaatcagtaatgactgttcttgtctacacagATTATAAATCTGCGTTCAATTAGGCCCCTGGACACACCCACGATCAATGCCTCAGTCAGGAAAACTAACAGACTTGTAACCGTTGAAGAAGGGTTCCCTC
















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|58608415|gb|CK036448.1|CK036448
EST:     GAGATACTTTCCAAGGAGGGAATCAGTGCTGACG                         GGGATCAATCTTCGGTCAATTAGGCGATTGGATAGAGCTACTATCAATGC
genomic: GAGATACTTTCCAAGGAGGGAATCAGTGCTGA-Ggtagtttcct ... cttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGC
EST: gi|33824375|gb|CF338004.1|CF338004
EST:     GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG                         GTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
genomic: GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAGgtagtttcct ... cttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
EST: gi|218478794|gb|FG960305.1|FG960305
EST:     TGCAGAGATACTTTTCCAAGGAGGGAATCAGTGCTGAG                         GTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
genomic: TGCAGAGATAC-TTTCCAAGGAGGGAATCAGTGCTGAGgtagtttcct ... cttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
EST: gi|87020958|gb|CI269675.1|CI269675
EST:     GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG                         GTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
genomic: GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAGgtagtttcct ... cttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
EST: gi|38472326|gb|CF956457.1|CF956457
EST:     GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG                         GTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
genomic: GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAGgtagtttcct ... cttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
EST: gi|33824376|gb|CF338005.1|CF338005
EST:     GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG                         GTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
genomic: GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAGgtagtttcct ... cttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
EST: gi|29614435|gb|CB619448.1|CB619448
EST:     GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG                         GTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
genomic: GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAGgtagtttcct ... cttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
EST: gi|38475005|gb|CF959138.1|CF959138
EST:     GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG                         GTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
genomic: GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAGgtagtttcct ... cttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
EST: gi|86854408|gb|CI256530.1|CI256530
EST:     CAGGCTGCAGAGATACTTTCCAAGGAGGGAATCAGTCCTGAG                         CTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
genomic: CAGGCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAGgtagtttcct ... cttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
EST: gi|86495018|gb|CI137651.1|CI137651
EST:     CTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG                         GTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA
genomic: CTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAGgtagtttcct ... cttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCA

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: 39 (upstream exon), 60 (downstream exon)
Score: 35

GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAGgtagtttcct ... cttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaacaacatgccatcactgttttcttattactatatatcaatatcttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCAC
 ttttaac  putative branch site (score: 35)
                                            tcttttatc  putative PPT
                  tgttttcttattacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtttccttttgcaaaatatactgtacagtatagatatgcaactagacatctatttttaacaacatgccatcactgttttcttattactatatatcaatatcttttatcagGTGATCAATCTTCGGTCAATTAGGCCATTGGATAGAGCTACTATCAATGCATCAGTTAGGAAAACCAACAGATTGGTAACCCTTGAAGAAGGATTTCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG