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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatatgggtaactttgttcaggttaactctgttgataactctgaattggcatctaaattctcgctttttcttttgcattggttgtgcctgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTGGACAACCAAGGAGATGTTCCCAATCATTCTCACCATATCGAGCTATGAA

Basic information

species Oryza sativa
transcript LOC_Os11g02464.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G347541_T02 (Zea mays), 3'ss of exon 5
gtatgatatgggtaactt------tgttcaggttaact--ctgttgataactctgaattggcatctaaattctcgcttt-ttcttttgcattggttgtgcctgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTGGACAACCAAGGAGATGTTCCCAATCATTCTCACCATATCGAGCTATGAA
||| ||||| || | | |        |    ||| | |  ||  ||||  |||          |||   ||  ||  |  |||| || |     |||  | ||| | |||||||||||||| || |||||||||||||||||||||||||||||||| ||||||| |||||||||||| |  |  ||  | |||||||| ||| | ||| 
gtaagatataggcagcctgtaatgcttctttgttcattgccttctgatggctcgctcgctcactctgggttggcgtctgattctgttcctgcatttgcccgtgtctgcagAGGTACATGGACTCGGAGATCCGCGCCATCATGGCCCAGTACATGCCTCTGGACAGCCAAGGAGATGTCCAGAGCCACGCGCACCATATTGAGATGTGAG

upper sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 12
--gtatgatatgggtaactttgttcaggttaact--ctgttgataactctgaattggcatctaaattctcgctttttcttttgcattggttgtgcctgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTGGACAACCAAGGAGATGTTCCCAATCATTCTCACCATATCGAGCTATGAA
     |  |||  |        |  | ||| | |  ||  ||||||||| |   ||||||||||        || |  | ||||||||  | |||||    ||||||||||||||| ||||||||||| ||||||||||| ||||||||||||||||||||||||||||| ||||  |  |||||||| |               
gtaagtagtatctgctgacacttgtatgttcattaccttctgataactcggg--tggcatctaa--------ttctgttcttgcattgcctatgcct----acagAGGTACATGGACTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCCCTGGACAACCAAGGAGACGTTCAGAGCCATTCTCATC---------------

upper sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 11
gtatgatatgggtaactttgttcaggttaactctgttgataactctgaattggcatctaaattctcgctttttcttttgcattggttgtgcctgtg----tacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTGGACAACCAAGGAGATGTTCCCAATCATTCTCACCATATCGAGCTATGAA
       |||| || ||   || | ||      ||    ||| |   |  ||| |     ||        ||   ||         | | | | ||    | ||||| ||||||||||| |||||  | || |||||||| |||||||||||  |||| || ||||||||  |||| ||||||  || ||||   ||  | |  |
----tgcatggatacctagattaatgtggtacgtgcctgtaattgctatatggaaataggatcaatatgattgtgttaatgacaact-tccttttgctgttgcagAGATACATGGATTCTGAGATTAGGGCAATCATGGCACAGTACATGCCTTTGGATAATCAAGGAGAGATTCCAAATCATGTTCCCCATGGGGACATTTAGA

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|89186216|gb|CI048085.1|CI048085
EST:     TACAGGATCCGG                         AGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCTCTG
genomic: TACAGGATCCGGgtatgatatg ... ctgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|88831436|gb|CI083830.1|CI083830
EST:     ATACAGGATCCGG                         AGGTACATGGATTCAGAGATCCGCGCCATCATGCCCCAGTACATGCCCCTG
genomic: ATACAGGATCCGGgtatgatatg ... ctgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|86852363|gb|CI319298.1|CI319298
EST:     GTAGCAGGCATTGCAGGATACGCAGTATACAAATACAGGATCCGG                         AGGTACATGTATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
genomic: GTAGCAGGCATTGCAGGATACGCAGTATACAAATACAGGATCCGGgtatgatatg ... ctgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|58608731|gb|CK036764.1|CK036764
EST:     TAGTGGTAGCAGGCATTGCAGGATACGCAGTATACAAATACAGGATCCGG                         AGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
genomic: TAGTGGTAGCAGGCATTGCAGGATACGCAGTATACAAATACAGGATCCGGgtatgatatg ... ctgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|3759628|gb|C96886.1|C96886
EST:     ACAAATACCAGGATCCGN                         AGGTNCATGGATTTCAGAGATCCGCGCCATCATGGCCCCAGTACATGCCCC
genomic: ACAAATA-CAGGATCCGGgtatgatatg ... ctgtgtacagAGGTACATGGA-TTCAGAGATCCGCGCCATCATGG-CCCAGTACATGCCCC
EST: gi|86436573|gb|CI118295.1|CI118295
EST:     TAGTGGTAGCAGGCATTGCAGGATACGCAGTATACAAATACAGGATCCGG                         AGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCGTG
genomic: TAGTGGTAGCAGGCATTGCAGGATACGCAGTATACAAATACAGGATCCGGgtatgatatg ... ctgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|88841784|gb|CI081040.1|CI081040
EST:     TATACAAATACAGGATCCGG                         AGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
genomic: TATACAAATACAGGATCCGGgtatgatatg ... ctgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
EST: gi|88841719|gb|CI080975.1|CI080975
EST:     TAGTGGTAGCAGGCATTGCAGGATACGCAGTATACAAATACAGGATCCGG                         AGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG
genomic: TAGTGGTAGCAGGCATTGCAGGATACGCAGTATACAAATACAGGATCCGGgtatgatatg ... ctgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTG

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: 68 (upstream exon), 71 (downstream exon)
Score: 14

TGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCTTTGGCCTAGTGGTAGCAGGCATTGCAGGATACGCAGTATACAAATACAGGATCCGGgtatgatatg ... ctgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTGGACAACCAAGGAGATGTTCCCAATCATTCTCACCATATCGAGCTATGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattggcatctaaattctcgctttttcttttgcattggttgtgcctgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTGGACAACCAAGGAGATGTTCCCAATCATTCTCACCATATCGAGCTATGAA
        atctaaa  putative branch site (score: 14)
                      tttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatatgggtaactttgttcaggttaactctgttgataactctgaattggcatctaaattctcgctttttcttttgcattggttgtgcctgtgtacagAGGTACATGGATTCAGAGATCCGCGCCATCATGGCCCAGTACATGCCCCTGGACAACCAAGGAGATGTTCCCAATCATTCTCACCATATCGAGCTATGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG