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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgttgcttacacttttagaataaacagatgaactatagggcgcgtgatttgtcactatagaagagtctctgaacaccatgctagtttcattcatttcagGAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAGCTACACAGCCATCTCAACTTCAAAGTACATCTGCCAATGTCCCTGTGCC

Basic information

species Oryza sativa
transcript LOC_Os02g08120.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 8
acgttgcttacacttttagaataaacagatgaactatagggcgcgtgat-ttgtcactatagaagagtc---tctgaacaccatgctagtttcattcatttcagGAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAGCTACACAGCCATCTCAACTTCAAAGTACATCTGCCAATGTCCCTGTGCC------------
  |||   |||  |  |    || |||   ||  | |||     || |  |  | | | |       |    | ||| | || ||||  ||| |||| |||||||            ||||||||||||| ||||||||| || | ||||| |||| ||||| | ||||||||| || ||| ||||  ||||| |||    |||            
-agtttgatacgatgctc---tagacattagacttgtagattttgttacatcattattgtgaggctttgaaatttgagcgccgtgcttctttaattcctttcagG------------TGGAACTGATTCCGTAGGGTATGGTGTCGACCAATCAGCAACACATCTATCTCAACTCCAGAGTTCATCCACCAATCTCCAGACGCCATACGATGACAC
















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|117244367|gb|CT849708.1|CT849708
EST:     ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAG                         GTGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAG
genomic: ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAGgttagaagca ... ttcatttcagGAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAG
EST: gi|29669563|gb|CB665838.1|CB665838
EST:     ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAGTTTCATTCATTTCAG           
genomic: ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCT-C--CAG------------CAGgttagaagca
EST: gi|51946147|gb|CV152488.1|CV152488
EST:     ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAG                         GAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAG
genomic: ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAGgttagaagca ... ttcatttcagGAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAG
EST: gi|87027680|gb|CI274244.1|CI274244
EST:     ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAG                         GAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAG
genomic: ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAGgttagaagca ... ttcatttcagGAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAG
EST: gi|29638015|gb|CB643024.1|CB643024
EST:     ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAG                         GAGGAAGTGGAACTGGAACTGATTCCATAGGGGGTGATGGCAACCAAGCAG
genomic: ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAGgttagaagca ... ttcatttcagGAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAG
EST: gi|58667942|gb|CK056628.1|CK056628
EST:     ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAG                         GAGGAAGTGGAACTGGAACTTGATTCCATAGGGTATGATGGGCAAC
genomic: ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAGgttagaagca ... ttcatttcagGAGGAAGTGGAACTGGAACT-GATTCCATAGGGTATGATGG-CAAC
EST: gi|29668781|gb|CB665056.1|CB665056
EST:     ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAG                         GAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAG
genomic: ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAGgttagaagca ... ttcatttcagGAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAG
EST: gi|55409522|gb|CV721898.1|CV721898
EST:     ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAG                         GAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAG
genomic: ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAGgttagaagca ... ttcatttcagGAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAG
EST: gi|29622551|gb|CB627562.1|CB627562
EST:     ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAG                         GAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAG
genomic: ATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAGgttagaagca ... ttcatttcagGAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAG

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: 45 (upstream exon), 43 (downstream exon)
Score: 3

GCACCCACTGGACACGTTGAGACACATCCTCCTCTGAGTCAACCTGCTTCATACGAACAACGCATCTCATCAGCGAGCATGACAGGACCATCTCCAGCAGgttagaagca ... ttcatttcagGAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAGCTACACAGCCATCTCAACTTCAAAGTACATCTGCCAATGTCCCTGTGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttgtcactatagaagagtctctgaacaccatgctagtttcattcatttcagGAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAGCTACACAGCCATCTCAACTTCAAAGTACATCTGCCAATGTCCCTGTGCC
                                        tttcattc  CT-rich tract
                                            attcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgttgcttacacttttagaataaacagatgaactatagggcgcgtgatttgtcactatagaagagtctctgaacaccatgctagtttcattcatttcagGAGGAAGTGGAACTGGAACTGATTCCATAGGGTATGATGGCAACCAAGCAGCTACACAGCCATCTCAACTTCAAAGTACATCTGCCAATGTCCCTGTGCC

- gttgctt
- - - - - - - - - gaataaa
- - - - - - - - - - - - - -gatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -atagaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgcta