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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtgccgggacttttaaagagttctattttctagtgtttcccattacatccttttggtataaactttaattaaacctcctctatgtttgcacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCAAATGAAACATATTGCTCACCAATCTTCACCTGCATGAGGCAATCGGGGT

Basic information

species Oryza sativa
transcript LOC_Os12g36180.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g36180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G12770.1 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------------------------------------------aagtgccggga-----cttttaaagagt-tctattttctagtgtttcccattacatccttttggtataaacttta-attaa--------acctcctctatgtttgcacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCT-AAACGGCCTGCGCAAATGAAACATATTGCTCACCAATCTTCACCTGCATGAGGCAATCGGGGT
                                                           | |  ||   |     |  ||| |  |  |||  |      ||  |   |  ||  |    | ||| ||| |  | |||||        | ||| | | |  |  ||  |||||||| |||||||||||||||||||||||||||||||| | |||   |||| |  ||||      |  |        || || |  ||  ||   |    |   
gtatgattcaacatctttctggaactaaatccatcactgctactttcagatgccaccaaaggaaccaaaaaaatccacttagactgcgtctcctcatggatgactagaagaaccgcacaattgtacaaaatccatattaactggcttgaactcttttctcatgacaataaacagGAAGCATGGAACAAATTCAACTCAGAGGAACTCTTTTGAAAAAACCTGAGATAATGTTTTTGAGAGTGTGTTGTTCGTCTCTAGCGCGAAAGATGAAGCA-

upper sequence: LOC_Os12g36180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G12780.1 (Arabidopsis thaliana), 3'ss of exon 7
----------------------------------------------aagtgccgggacttttaaagagttctattttctagtgtttcccattacatccttttggtataaactt--taattaaacctcctctatgtttgcacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCAAATGAAACATATTGCTCACCAATCTTCACCTGCATGAGGCAATCGGGGT
                                                  || |  ||    |||      |   || ||    |  |      ||  | |   |  | | ||  |   | || ||||| | |  |  ||  |||||||| ||||||||||| || |||||||| |||||||||| |         |    |      |            || |   | ||   |   |       |
gtaagtgaattcaccatttttctggaaataaatccatcactgctacttcagctgccaccgacaaaacaccttgcattttacgaataactgcacaattgtataaatccacatttgctggcttaatctcctttgtcatgacaataaacagGAAGCATGGAACAAGTTTAACTCAGAAGAACTCTTCTGAGGAAATCATGGGGCTATGTTTTGAGATGTGTTTTTCGTGTGCCGCCCAAAAGATGATACAT
















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|88693872|gb|CI735449.1|CI735449
EST:     CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
EST: gi|2798949|gb|AA752243.1|AA752243
EST:     CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGACCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
EST: gi|29669275|gb|CB665550.1|CB665550
EST:     CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
EST: gi|88690893|gb|CI734972.1|CI734972
EST:     CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
EST: gi|66929165|gb|CX116013.1|CX116013
EST:     CAATTCTACACCAGAGATATGTTGCCGAGAAGGTG-TTGATCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
EST: gi|88232794|gb|CI232038.1|CI232038
EST:     CAAATTTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
EST: gi|88691955|gb|CI735530.1|CI735530
EST:     CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
EST: gi|218489008|gb|FG952445.1|FG952445
EST:     CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
EST: gi|88689066|gb|CI732642.1|CI732642
EST:     CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
EST: gi|33683328|gb|CF311567.1|CF311567
EST:     AAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTTGATCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: AAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTT-GATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
EST: gi|29669274|gb|CB665549.1|CB665549
EST:     CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
EST: gi|88230575|gb|CI230451.1|CI230451
EST:     CCGAGAAGGTGTTTGATCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: CCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
EST: gi|38469324|gb|CF953455.1|CF953455
EST:     CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
EST: gi|88689029|gb|CI732605.1|CI732605
EST:     CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
EST: gi|87031795|gb|CI272496.1|CI272496
EST:     CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAG                         GAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA
genomic: CAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCA

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: 73 (upstream exon), 74 (downstream exon)
Score: 19

TAGAAAGGCAACATTGTGCATACATCCTGACAAGGTGCAGCAAAAGGGGGCAAATCTACAGCAGAAATATGTTGCCGAGAAGGTGTTTGATCTCCTTAAGgtgtgtatgc ... cacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCAAATGAAACATATTGCTCACCAATCTTCACCTGCATGAGGCAATCGGGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatccttttggtataaactttaattaaacctcctctatgtttgcacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCAAATGAAACATATTGCTCACCAATCTTCACCTGCATGAGGCAATCGGGGT
                   ctttaat  putative branch site (score: 19)
       ttttggtataaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtgccgggacttttaaagagttctattttctagtgtttcccattacatccttttggtataaactttaattaaacctcctctatgtttgcacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCTAAACGGCCTGCGCAAATGAAACATATTGCTCACCAATCTTCACCTGCATGAGGCAATCGGGGT

- gtgccgg
- - - - - - - - - - - - - - - - - - - - - - -tacatcc