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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgctcgtcaaattctttgcttctcaatttaaatataactgtgctacaggtgcttgcgctattccaacttgctgcaacatgctcatctgaactgttaatgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAG

Basic information

species Oryza sativa
transcript LOC_Os06g09290.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 2
gtgtgtgctc-gtcaaattctttgcttctcaatttaaatataactgtgctacaggtgcttgcgctattccaacttgctgcaacatgctc---atctgaactgttaatgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAG
    || |||  ||||||     | |  || ||| |     | |||   || |||   ||  |    |||   |||    | ||| |     || ||  ||  || | ||  ||||| || || |||||||| || ||  ||||||||||||||||||||||  | || || ||||||||||||||||| || || |||||  | || 
---agttctctatcaaat-----gttcttccattca---tcagctgctttaaagg---ttaagaaggtcct-tttgaattagcatacctgagatgtgccctcatacttaac-gcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 2
gtgtgtgctcgtcaaattctttgcttctcaatttaaatataactgtgctacaggtgcttgcgctattccaacttgctgcaacatgctcatctgaactgttaatgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAG
     |  | |  |  ||      ||    |||    | ||| ||  |   |  ||| | |  | ||      |  || || ||| |    |   || ||  ||  ||| ||| || || |||||||| ||||| || ||| |||| ||||||||||| ||||| || ||||| || ||||||||||||||||| || || |||
---gataattggtattttggggatttgctgatt--gttttaattgcaca--aactgcatacaatcttgtgtacttttgtaa-atgttagattt--cttttgttg--ttgtagGTATCAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 2
gtgtgtgctcgtcaaattctttgcttctcaatttaaatataactgtgctacaggtgcttgcgctattccaacttgctgcaacatgctcatctgaactgttaatgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAG
    ||     | | ||| | ||||  |     ||| |  |      |||  | || |  | || | | ||| | ||  ||  |   | ||   | |||||         ||| || || |||||||| |||||||| ||  |||| ||||||||||| ||||| || |||||||| ||||||||||| ||||| || || |||
----gttgcatttatattttatgctgattgtcctaattgcacggaatctat-gctgttaacact-tgcaaacctcctcaaatgttagcttcctga-tgtta-----caatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 2
gtgtgtgctcgtcaaattctttgcttctcaatttaaatataactgtgctacagg-tgcttgcgctattccaacttgctgcaacatgctcatctgaactgttaatgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAG
    ||     | | | | | | ||  |     ||| | ||  ||  ||  | | || |  | ||  | || ||   |   | ||| |    |   |||||  |  | |  ||| || || |||||||| ||||| || ||| |||| ||||||||||| ||||| || |||||||| ||||||||||||||||| || || |||
----gttgcatttatagtttatactggttgtcctaattgta--tggactggatgctgttaacacttgtacacctcctt---aaatgtttgcttc--ctgttgttacaat--agGTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 2
-gtgtgtgctcgtcaaattctttgcttctcaatttaaatataactgtgctacaggtgcttgcgctattccaacttgctgcaacatgctcatctgaactgttaatgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAG
  |   || |  |       ||||||  | |  |||| |  |       || |  ||| | |  | ||      |  || || ||| |    |   || ||  ||  ||| ||| || || |||||||| ||||| |||||| |||| ||||||||||| ||||| || ||||| || ||||||||||||||||| || || |||
gataattggtattttggggatttgctgattatcttaattgca-------ta-aactgcatactgtcttgtgtacttttgtaa-atgttagattt--cttttgttg--ttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------------------------------------------------gtgtgtgctcgtcaaattcttt---gcttctcaatttaaatataactgtgctacagg-tgcttgcg-ctattccaacttgctgcaacatgctcatctgaactgttaatgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAG
                                                                                    ||  | | |||  |  |    |    |    | || ||    |||  ||  || || ||  | ||     |||        | ||  |       | | | |    ||  |||| || || || ||||| ||||| || ||| |||| || |||||||| ||||| || |||||||| ||||||||||||||||| || || |||
gtatgtttcttattcgtgatatttccaatgtatagtgctatttgataaactgggcatgtattatgttgatccatgttgaaaatagtagtagccaaggttatatgagaagttttgataaactaggcatgtattatgggctgattatggcttgaataacacttcatgaaattatagcaatgattttcatcttataacagGTATCAAGGAATCTGATACTGGCTTAGCTGCACCAAGTCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 2
gtgtgtgctcgtcaaattctttgcttctcaatttaaatataactgtgctacaggt-gcttgcg-ctattccaacttgctgcaacatgctcatctgaactgttaatgaatt-gcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAG
  || ||   |   || | |||| |      |   |||||   ||||  |||  | |||| |  || || | | ||  |     |   | |  ||   ||| |  | ||  |||||||| |||||||| ||||| ||  ||||    ||||| |||||||| || ||||| ||||||||||||||||| ||||| |||||  |||||
--gtatgtagg---aactgtttgat----ggtcctaatat---tgtgtgacatttcgcttacctctctttccatttagtttctaagagttagttg---tgtcacggcatgagcagGAATCAAAGAGTCCGACACCGGGCTGGCAGTGCCTAGTCAGTGGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAG

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|58653641|gb|CK042321.1|CK042321
EST:     GGTTGAGAAGGAAATCAAAGAGATGGCGAAGAAGATAAATGATCTCTGTG                         GAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTGG
genomic: GGTTGAGAAGGAAATCAAAGAGATGGCGAAGAAGATAAATGATCTCTGTGgtgtgtgctc ... tgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTG
EST: gi|29666226|gb|CB662501.1|CB662501
EST:     GGTTGAGAAGGAAATCAAAGAGATGGCGAAGAAGATAAATGATCTCTGTG                         GAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTG
genomic: GGTTGAGAAGGAAATCAAAGAGATGGCGAAGAAGATAAATGATCTCTGTGgtgtgtgctc ... tgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcgctattccaacttgctgcaacatgctcatctgaactgttaatgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAG
                                       tgttaat  putative branch site (score: 3)
                                         ttaatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgctcgtcaaattctttgcttctcaatttaaatataactgtgctacaggtgcttgcgctattccaacttgctgcaacatgctcatctgaactgttaatgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG