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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA

Basic information

species Oryza sativa
transcript LOC_Os06g05180.2
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 20
gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatct-atgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA
      ||| ||| |||||||||| || || |||   || | ||        ||| | | |||||| | ||||  |||||| | ||| || ||||||||||||||||| ||| |||| ||||| |||||||| ||||||||  | |||||||| ||||| |||||| | ||||| ||||||
------gtaaatcttgtttgctgtgattaaatccttgttttggtgctcttcctttgagaactaaacattatcttgtgtattctgcagTAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAAAGTACCAGAGATAGTGGCAATTTGGAGAGACGACCTGAGTAAA

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 19
gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatcta-tgtatta-----tacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA
      |||  || |||||||||| || || |||   || | ||        ||| | |||||||| | ||||  ||||||      | ||| |  |||||||||||||||||  ||||||| || || |||||||| ||||||||  | || ||||||||||| |||||||| ||||||||||||
------gtaagtcttgtttgctgtgattaaatccttgttctggtgctgttcctttgagagctaaacattatcttctgtattcggcactgcagTAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 5
gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatct-atgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA
      ||| ||| |||||||||| || || |||   || | ||        ||| | | |||||| | ||||  |||||| | |||||| ||||||||||||||||| ||| |||| ||||| |||||||| ||||||||  | |||||| | ||||| |||||| | ||||| ||||||
------gtaaatcttgtttgctgtgattaaatccttgttttggtgctcttcctttgagaactaaacattatcttgtgtattctgcagCAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAAAGTACCAGAGATATTGGCAATTTGGAGAGACGACCTGAGTAAA

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 20
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattat-acagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA
    || |   | |||||  ||     |        | |  | ||  |   ||||   | ||  |   ||   |  |||  | |||| || || ||||| ||||||||  | |||||||||||||||||||| ||||||||||| |||||||||||  |||||||  | || ||||| || 
--gtatttcattactgttcacttggccgtttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 20
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 20
---gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA
    | |||    |  |  ||    |||  |||   |  |||    |  | | ||  | ||  ||      ||  ||| | ||   ||| || || ||||| ||||||||  | |||||||| || |||||||| |||||||||||||||||||||||  | ||||| || || ||||| || 
gtaattcattagtagtcacttgagagtttggaaaatcaaattt--atgcacctttggttaa--ctgtgtgacaa-tattttttcctcagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 20
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
---------------------------------------------------------------------------gtacatgtacatcctgtttgctgtt-atgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA
                                                                            |  |   |||   || | |  ||| ||     ||     || |  | | | ||| |  |    |  || || |  || |  | ||| ||||| |||||||||||||| ||||||||||| ||||| ||||| ||||| ||| | |||||| |  | || ||||||||||||||||  || 
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatg-gtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 20
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 20
gtacatgtacatcctgtttgctgttatgaactcc----ccattgtagtaa-atcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA
|||  |||   |  |   |||    |||    |        |||| |  | ||     ||    | | |  || |   ||    | | ||||||||| || ||||| ||||| || |||||||| ||||||||||| ||||| || || |||||||| ||  | ||||| || ||||| | ||| 
gtaattgt-tgttgttactgcaaacatgggaacaaagatagttgtggagatattccacttttgggatgatactgaagcattctctttgcagCAATCGGATCCCTGAGGCTGCTTTGATGGCACGGTCTTATCTTCCAAGCAAGGTCTCAGAGATAGTCGCTCTGTGGAGGAAAGACCTTAATAAG

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|58658342|gb|CK047022.1|CK047022
EST:     CTCGTTATGCTTGGTAAATTGGAAGATTGCATACAATTGCTGATAGACAG                         CAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAA
genomic: CTCTTTATGCTTGGTAAATTGGAAGATTGCATACAATTGCTGATAGACAGgtacatgtac ... tattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAA
EST: gi|58665864|gb|CK054550.1|CK054550
EST:     CAATTGCTGATAGACAG                         CAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAA
genomic: CAATTGCTGATAGACAGgtacatgtac ... tattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAA
EST: gi|2310301|gb|C26456.1|C26456
EST:     CTCTTTATGCTTGGTAAATTGGAAGATTGCATACAATTGCTGATAGACAG                         CAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAA
genomic: CTCTTTATGCTTGGTAAATTGGAAGATTGCATACAATTGCTGATAGACAGgtacatgtac ... tattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAA

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: 69 (upstream exon), 37 (downstream exon)
Score: 40

TTGCTTCTCAAGCAAAGGAGCATGGCAAAAACAATGTTGCTTTCCTCTGTCTCTTTATGCTTGGTAAATTGGAAGATTGCATACAATTGCTGATAGACAGgtacatgtac ... tattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA
                           agctaaa  putative branch site (score: 40)
            taaatcatttttcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA