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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atccaaggtacatgcactatttagttcttttttaatttggtaatcaccattctgcgattctgaaagacaaacatttcatttggactaatctcttcagcagGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGACGAGATACACCTGGATGTACAAAGCCTTCTCAAGTTGGTGTAATGCTATTTAT

Basic information

species Oryza sativa
transcript LOC_Os07g08880.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G097726_T02 (Zea mays), 3'ss of exon 4
--atccaaggtacatgcact----atttagttcttttttaatttggtaatcaccattctgcgattctgaaagacaaacatttcatttggactaatctcttcagcagGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCA-TTGACGAGAT--ACACCTGGATGTACAAAGCCTTCTCAAGTTGGTGTAATGCTATTTAT
  || |||    || |        |   ||  |  | | ||      |||    |||  |   || ||      ||   | | | ||  ||| ||||||||||| ||||||||||||||| ||| ||||||||  |||   | |||| | || | || ||  |  |  || |||||||||||||| || |||    | | | |      
gcattcaaacatcaagtgaggggaaccaagcaccctctaaaaactacaatgtgaatt--gtagttatgcttc-taatagtataactttaactgatctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTATGAAATCTATGCTCGGTTGTACAAAGCCTTCCCACGTT----TCACGTTTGAG--
















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|88852528|gb|CI374296.1|CI374296
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGCAG                       
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAG-AAA--AGgtaaaatatg ... tcttcagc
EST: gi|218504563|gb|FG952376.1|FG952376
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         C
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... tcttcagcag-
EST: gi|218504563|gb|FG952376.1|FG952376
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         C
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... tcttcagcag-
EST: gi|218504563|gb|FG952376.1|FG952376
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         C
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... tcttcagcag-
EST: gi|88907070|gb|CI376142.1|CI376142
EST:     CTCATGAAGCTACAGCGCAATCCGAAGAAAAGCAG                       
genomic: CTCATGAAGCTACAGCGCAATCCGAAG-AAA--AGgtaaaatatg ... tcttcagc
EST: gi|86531645|gb|CI171851.1|CI171851
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGCAG                       
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAG-AAA--AGgtaaaatatg ... tcttcagc
EST: gi|86261244|gb|CI014311.1|CI014311
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGCAG                       
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAG-AAA--AGgtaaaatatg ... tcttcagc
EST: gi|89178885|gb|CI391883.1|CI391883
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         GTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGACGAG
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... tcttcagcagGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGACGAG
EST: gi|88438337|gb|CI541081.1|CI541081
EST:     ATCCGAAGAAAAGCAG                       
genomic: ATCCGAAG-AAA--AGgtaaaatatg ... tcttcagc
EST: gi|88831715|gb|CI369397.1|CI369397
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGCAG                       
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAG-AAA--AGgtaaaatatg ... tcttcagc
EST: gi|88261442|gb|CI365018.1|CI365018
EST:     AGATGGCTGAGAATTCTCATTAAGCTACAGCGCAATCCGAAGAAAAGCAG                       
genomic: AGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAG-AAA--AGgtaaaatatg ... tcttcagc
EST: gi|88201730|gb|CI202085.1|CI202085
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGCAG                       
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAG-AAA--AGgtaaaatatg ... tcttcagc
EST: gi|218495783|gb|FG965861.1|FG965861
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGCAG                       
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAG-AAA--AGgtaaaatatg ... tcttcagc
EST: gi|86498011|gb|CI140644.1|CI140644
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGCAG                       
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAG-AAA--AGgtaaaatatg ... tcttcagc
EST: gi|86544705|gb|CI184911.1|CI184911
EST:     AGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGTAAAGCAG                         GTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGACGA
genomic: AGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAG-AAA--AGgtaaaatatg ... tcttcagcagGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGACGA
EST: gi|89178434|gb|CI015139.1|CI015139
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGCAG                       
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAG-AAA--AGgtaaaatatg ... tcttcagc
EST: gi|29686487|gb|CB682762.1|CB682762
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAG                         GTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGACGAG
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... tcttcagcagGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGACGAG
EST: gi|88964512|gb|CI055208.1|CI055208
EST:     GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGCAG                       
genomic: GAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAG-AAA--AGgtaaaatatg ... tcttcagc
EST: gi|88838617|gb|CI376155.1|CI376155
EST:     CTGAGGATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGCAG                       
genomic: CTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAG-AAA--AGgtaaaatatg ... tcttcagc

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: 19 (upstream exon), 75 (downstream exon)
Score: 3

TGCAAAAAAACTAGAGCATTTTTTCTGCCAGAGCTGTACTGCGGAAAATGGAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatg ... tcttcagcagGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGACGAGATACACCTGGATGTACAAAGCCTTCTCAAGTTGGTGTAATGCTATTTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accattctgcgattctgaaagacaaacatttcatttggactaatctcttcagcagGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGACGAGATACACCTGGATGTACAAAGCCTTCTCAAGTTGGTGTAATGCTATTTAT
                                     gactaat  putative branch site (score: 3)
                                           tctcttc  CT-rich tract
                           atttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atccaaggtacatgcactatttagttcttttttaatttggtaatcaccattctgcgattctgaaagacaaacatttcatttggactaatctcttcagcagGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCATTGACGAGATACACCTGGATGTACAAAGCCTTCTCAAGTTGGTGTAATGCTATTTAT

- - - - tacatgc
- - - - - - - - - - - - - - - - - - - - - - - - attctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaaca