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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtacgtactgccgctccggcaataatgcgtaccagtactattttcgtcgcaatgtggttgtgtggaggtgatttgttagcgataagtggcctgatcagcgaggcgaatccgatgcagGTGGTCGCAAATCGCGTCGCACTTGCCGGGGAGGACGGACAACGAGATCAAGAACTTCTGGAACAGCTGCCTCAAGAAGAAGCTGAGGCAGCGCGGCATC

Basic information

species Oryza sativa
transcript LOC_Os01g50720.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50720.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G003406_T01 (Zea mays), 3'ss of exon 2
gttcgtacgtactgc-cgctccggcaataatgcgtaccagtactattttcgtcgcaatgtggttgtgtggaggtgatttgttagcgataagtggcctgatcagcgaggcgaatccgatgcagGTGGTCGCAAATCGCGTCGCACTTGCCGGGGAGGACGGACAACGAGATCAAGAACTTCTGGAACAGCTGCCTCAAGAAGAAGCTGAGGCAGCGCGGCATC
    ||||||||    || ||||| |  ||      | | |  | |  |   | ||  |  || | | || || |    |   || || | ||   |  |   || ||         |||||||||||||| ||||||||||||||||||||  ||||||||||||||||||||||||||||||||||||||||||||||||||||| | ||||||||||||
----gtacgtacaatgcgttccgg-accaac-----caactgatctccttacc-cagcgcagt-gggcggcggcg-cgcggcggc-atcaatgtatttcttttcgcgg--------gtgcagGTGGTCGCAGATCGCGTCGCACTTGCCGGGCCGGACGGACAACGAGATCAAGAACTTCTGGAACAGCTGCCTCAAGAAGAAGCTGCGTCAGCGCGGCATC

upper sequence: LOC_Os01g50720.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
gttcgtacgtactgccgctccggcaataatgcgtaccagtactattttcgtcgcaatgtggttgtgtggaggtgatttgttagcgataagtggcctgatcagcgaggcgaatccgatgcagGTGGTCGCAAATCGCGTCGCACTTGCCGGGGAGGACGGACAACGAGATCAAGAACTTCTGGAACAGCTGCCTCAAGAAGAAGCTGAGGCAGCGCGGCATC-
          |     | | | |    ||  | |   | |  |      |   |||  | ||| | |  |  |  ||  ||    | || | | |  ||| | | | |        ||||||||||| || || ||  | ||  | || ||  | ||||||||||||||||||||||||||||||   ||| |||||||||||||  | ||||  || |   
---------gatgagagattctgt--caacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaa-aattagtc-aatcggtgggtc--------tgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCG-CAGCATGGGAATC
















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|701072|gb|D47363.1|D47363
EST:     CAGCAGGAGGAGGACGCCATCGTCGGCCTNCATGAGATCCTAGGCAACAG                         GTGGTCGCAAATCGCGTCGNACTTTCCGGGGAGGACGGACAACGAGATCAA
genomic: CAGCAGGAGGAGGACGCCATCGTCGGCCTGCATGAGATCCTAGGCAACAGgttcgtacgt ... tccgatgcagGTGGTCGCAAATCGCGTCGCACTTGCCGGGGAGGACGGACAACGAGATCAA
EST: gi|88742125|gb|CI765633.1|CI765633
EST:     CAGCAGGAGGAGGACGCCATCGTCGGCCTGCATGAGATCCTAGGCAACAG                         GTGGTCGCAAATCGCGTCGCACTTGCCG
genomic: CAGCAGGAGGAGGACGCCATCGTCGGCCTGCATGAGATCCTAGGCAACAGgttcgtacgt ... tccgatgcagGTGGTCGCAAATCGCGTCGCACTTGCCG
EST: gi|88735991|gb|CI759499.1|CI759499
EST:     CAGCAGGAGGAGGACGCCATCGTCGGCCTGCATGAGATCCTAGGCAACAG                         GTGGTCGCAAATCGCG
genomic: CAGCAGGAGGAGGACGCCATCGTCGGCCTGCATGAGATCCTAGGCAACAGgttcgtacgt ... tccgatgcagGTGGTCGCAAATCGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaggtgatttgttagcgataagtggcctgatcagcgaggcgaatccgatgcagGTGGTCGCAAATCGCGTCGCACTTGCCGGGGAGGACGGACAACGAGATCAAGAACTTCTGGAACAGCTGCCTCAAGAAGAAGCTGAGGCAGCGCGGCATC
                          gcctgat  putative branch site (score: 4)
        atttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtacgtactgccgctccggcaataatgcgtaccagtactattttcgtcgcaatgtggttgtgtggaggtgatttgttagcgataagtggcctgatcagcgaggcgaatccgatgcagGTGGTCGCAAATCGCGTCGCACTTGCCGGGGAGGACGGACAACGAGATCAAGAACTTCTGGAACAGCTGCCTCAAGAAGAAGCTGAGGCAGCGCGGCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA