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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacatctaccaccctttatttcctcactttttagttatcatatggccacatgtgggacttgcacctgatacataattgagttgctaactggattcaatctgtgccatgatgcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTGGATAACCAAGAAGCAGCTAACCAACATCATGTCGCGCATGCTGGTGATG

Basic information

species Oryza sativa
transcript LOC_Os03g21720.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21720.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G067546_T01 (Zea mays), 3'ss of exon 11
gtaaaacatct-accaccctttatttcctc----actttttagttatcat------atggccacatgtgg----gacttgc-acctgatac-ataattgagttgctaactggattcaatctgtgccatgatgcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTGGATAACCAAGAAGCAGCTAACCAACATCATGTCGCGCATGCTGGTGATG
|||||||| || || |    | | || ||     ||  |||  |  | ||       ||| | ||||| |    || |||| |  || |||   |||   | |||       | | || |  |           ||| ||||| ||||||||||| ||||| || || |||||||| |||||||||||| ||||||||||||||| ||| ||||| ||||| |||| ||| ||   |||| 
gtaaaacaactcacgatttctcagtttcttctctaccctttgatctttatttgcaagtggtcgcatgtagacttgatttgctagttgttactgcaataatgatgcatttgttactgaaaccttttgtcatcatttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTGGATAACCAAGAAGGAGCAAACCAGCATCAGGTCGTGCACGCCAATGATA

upper sequence: LOC_Os03g21720.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ30872 (Selaginella moellendorffii), 3'ss of exon 11
gtaaaacatctaccaccctttatttcctcactttttagttatcatatggccacatgtgggacttgcacctgat-acataattgagttgctaactggattcaatctgtgccatgatgcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTGGATAACCAAGAAGCAGCTAACCAACATCATGTCGCGCATGCT-GGTGATG
                                                       ||   |      | ||||  | | ||  ||     ||||  |     |||     |   |    |   ||   |||||||||||||||||| | || |||||||| |||||||||||  | || | |||| | |  |   | || ||       | | ||||| | |  | 
-------------------------------------------------------gtaatatcaattcgtgattgcttgatccagcaa--aacttaacgttctctactggaaacttttcctgtagTCTTACATGGATTCGGAGATTAGAGCTATCATGGCACAGTACATGCCGCTCGACAGCCAAAACGATGTGCATCACCACTTGCAAGAGGATGCTTGATTGT-

upper sequence: LOC_Os03g21720.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ31111 (Selaginella moellendorffii), 3'ss of exon 10
gtaaaacatctaccaccctttatttcctcactttttagttatcatatggccacatgtgggacttgcacctgatacataattgagttgctaactggattcaatctgtgccatgatgcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTGGATAACCAAGAAGCAGCTAACCAACATCATGTCGCGCATGC-TGGTGATG
                                                      |  | ||  |    |||  |   | |   |||| ||       |  | |||||          |   |||   || ||||||||||||||| | ||||||||||| |||||||||||| |||| | |||  | | ||   |||  || |  |  | | | || | ||||| 
-----------------------------------------------------gtacgtgatctct--ctggcattcattccggttggta-------ttgagctgtgtggctgctggttggcagTCTTATATGGATTCGGAGATTAGAGCGATCATGGCGCAGTACATGCCTCTGGACAGCCAGAACGAAGTCCACCGCCACCTCGAGGAGGAAGCGTAGTGAT-

upper sequence: LOC_Os03g21720.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ06539 (Selaginella moellendorffii), 3'ss of exon 10
gtaaaacatctaccaccctttatttcctcactttttagttatcatatggccacatgtgggacttgcacctgatacataattgagttgctaactggattcaatctgtgccatgatgcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTGGATAACCAAGAAGCAGCTAACCAACATCATGTCGCGCATGC-TGGTGATG
                                                      |  | ||  |    |||  |   | |   |||| ||       |  | |||||          |   |||   || ||||||||||||||| | ||||||||||| |||||||||||| |||| | |||  | | ||   |||  ||||  |  | | | || | ||||| 
-----------------------------------------------------gtacgtgatctct--ctggcattcattccggttggta-------ttgagctgtgtggctgctggttggcagTCTTATATGGATTCGGAGATTAGAGCGATCATGGCGCAGTACATGCCTCTGGACAGCCAGAACGAAGTCCACCGCCATCTCGAGGAGGAAGCGTAGTGAT-

upper sequence: LOC_Os03g21720.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ22768 (Selaginella moellendorffii), 3'ss of exon 11
gtaaaacatctaccaccctttatttcctcactttttagttatcatatggccacatgtgggacttgcacctgat-acataattgagttgctaactggattcaatctgtgccatgatgcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTGGATAACCAAGAAGCAGCTAACCAACATCATGTCGCGCATGCT-GGTGATG
                                                       ||   |      | || |  | | ||  ||     ||||  |     |||     |   |    |   ||   |||||||||||||||||| | || |||||||| |||||||||||  | || | |||| | |  |   | || ||       | | ||||| | |  | 
-------------------------------------------------------gtaatatcaattcgtgctcgcttgatccagcaa--aacttaacgttctctactggaaacttttcctgtagTCTTACATGGATTCGGAGATTAGAGCTATCATGGCACAGTACATGCCGCTCGACAGCCAAAACGACGTGCATCACCACTTGCAAGAGGATGCTTGATTGT-

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|29627369|gb|CB632380.1|CB632380
EST:     TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|29642136|gb|CB647143.1|CB647143
EST:     TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|87010695|gb|CI312387.1|CI312387
EST:     TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|86887736|gb|CI311869.1|CI311869
EST:     CGGAGCATAATNCGGTGTATAAATACAGGNTACGG                         AGNTANATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: CGGAGCAT-ATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|13165155|gb|AU173952.1|AU173952
EST:     AATACAGGCTACGG                         N
genomic: AATACAGGCTACGGgtaaaacatc ... gcctcatcag-
EST: gi|13165155|gb|AU173952.1|AU173952
EST:     AATACAGGCTACGG                         N
genomic: AATACAGGCTACGGgtaaaacatc ... gcctcatcag-
EST: gi|86865660|gb|CI335401.1|CI335401
EST:     TATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: TATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|88254724|gb|CI353548.1|CI353548
EST:     CGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: CGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|88989091|gb|CI042204.1|CI042204
EST:     TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|29665177|gb|CB661452.1|CB661452
EST:     TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|86882960|gb|CI314225.1|CI314225
EST:     TGCGGTGTATAAATACAGGCTACGG                         AGCGACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATCCCTTTG
genomic: TGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|29663536|gb|CB659811.1|CB659811
EST:     TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|18386961|gb|BM420159.1|BM420159
EST:     TTGTTC-TGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|58687228|gb|CK075915.1|CK075915
EST:     TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|38479499|gb|CF963610.1|CF963610
EST:     TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|88206350|gb|CI206199.1|CI206199
EST:     TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|218494604|gb|FG959186.1|FG959186
EST:     TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AAGCTACATGGATTCGGAGATACGCGCGATCATGGCCCAGTACATGCCTTT
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagA-GCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTT
EST: gi|86871404|gb|CI329801.1|CI329801
EST:     CTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTT-
genomic: CTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|87005715|gb|CI316134.1|CI316134
EST:     TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|300215578|gb|HO088204.1|HO088204
EST:     TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|14571249|gb|BI118617.1|BI118617
EST:     TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGT
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGT
EST: gi|18385663|gb|BM418862.1|BM418862
EST:     TTGTTCTT-CTGGGGTCGGAGCATAT-CGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCCGTACATGCCTTTG
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
EST: gi|86902901|gb|CI312278.1|CI312278
EST:     TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGG                         AGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG
genomic: TTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTG

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: 75 (upstream exon), 73 (downstream exon)
Score: 66

GGCTACGTCAGCTGTTGGCTGGAGTTTTCTGTGGGTTATTTTCTTTGGACTTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAGGCTACGGgtaaaacatc ... gcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTGGATAACCAAGAAGCAGCTAACCAACATCATGTCGCGCATGCTGGTGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatacataattgagttgctaactggattcaatctgtgccatgatgcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTGGATAACCAAGAAGCAGCTAACCAACATCATGTCGCGCATGCTGGTGATG
                tgctaac  putative branch site (score: 66)
                                              cctcatc  putative PPT
      ataattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacatctaccaccctttatttcctcactttttagttatcatatggccacatgtgggacttgcacctgatacataattgagttgctaactggattcaatctgtgccatgatgcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTGGATAACCAAGAAGCAGCTAACCAACATCATGTCGCGCATGCTGGTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG