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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacaccatagctagctagctagcttgagagtggccagccatggcggctctgagaatgacggcggatggggatcgagctgatggtcgctcgccggcgttcatggcgattatatatgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAGAAGAACGCCGGGCCGAACGCCAACTCGCTGCGCGGATTCGAGGTCATCG

Basic information

species Oryza sativa
transcript LOC_Os02g14160.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g14160.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G405459_T01 (Zea mays), 3'ss of exon 1
gtaagtacaccatagctagctagctagcttgagagtggccagccatggcggctctgagaatgacggcggatggggatcgagctgatggtcgctcgccggcgttcatggcgattatatatgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAGAAGAACGCCGGGCCGAACGCCAACTCGCTGCGCGGATTCGAGGTCATCG
    ||| | |||   |  |  |    ||||     |||  ||  ||  ||   | || ||| || ||    | |  | | |       | |||        | ||    |||    |||    ||||||||||||||||| ||||| || ||||||||| ||||| | || || ||||||||||| ||||| ||||||||||| |||||||| |||||||||||||
----gta-agcatgcatgtcgtggcgccttg-----ggcttgc--tgctggtcgtcagtatg-cgtcgcgccgcg--ccatccatccaacactccattattattattattattgcccatg----cagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAGAAGAACGCGGGGCCCAACGCCAACTCCCTGCGCGGCTTCGAGGTCATCG
















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|88743568|gb|CI767076.1|CI767076
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAT                         GGGTGCGACGCGTCGGTGCTGCTGGACGACTCG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCG
EST: gi|58656413|gb|CK045093.1|CK045093
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAT                         GGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG
EST: gi|58671450|gb|CK060136.1|CK060136
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAT                         GGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG
EST: gi|88745223|gb|CI768583.1|CI768583
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAT                         GGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCG
EST: gi|58654371|gb|CK043051.1|CK043051
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAT                         GGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG
EST: gi|13447542|gb|AU181036.1|AU181036
EST:     GCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAT                         GGGTGCGACGCAGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGA
genomic: GCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGC-GTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGA
EST: gi|58593599|gb|CF991907.1|CF991907
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAT                         GGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAG

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: 73 (upstream exon), 58 (downstream exon)
Score: 3

GCAGTCCATCGTGAGGTCGGCCATGGCGGCCGCCGTGCAGCAAGAGCCCCGCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacac ... atgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAGAAGAACGCCGGGCCGAACGCCAACTCGCTGCGCGGATTCGAGGTCATCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggatcgagctgatggtcgctcgccggcgttcatggcgattatatatgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAGAAGAACGCCGGGCCGAACGCCAACTCGCTGCGCGGATTCGAGGTCATCG
       agctgat  putative branch site (score: 3)
                                      attatatatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtacaccatagctagctagctagcttgagagtggccagccatggcggctctgagaatgacggcggatggggatcgagctgatggtcgctcgccggcgttcatggcgattatatatgattgcagGGGTGCGACGCGTCGGTGCTGCTGGACGACTCGTCGACGATCACCGGCGAGAAGAACGCCGGGCCGAACGCCAACTCGCTGCGCGGATTCGAGGTCATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC