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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattacatggtcgaccatcattttcaccttccataatttgcaaagatcaccggaaatcctcatatcttgttgttccaccatgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG

Basic information

species Oryza sativa
transcript LOC_Os03g55590.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g55590.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G171468_T02 (Zea mays), 3'ss of exon 3
-gtatattacatggtcgaccatc-attttcaccttccataatttgcaaagatcaccggaaatcctcatatc----------------------ttgttgttccaccatga---ttgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG
   | | |    |  ||| |  | |  || |||  |  |||||||   | || |    || | | |   ||                      |    | ||   ||||    ||||||| |||||||| || || ||||||||||||||| | || || ||||| || ||||| |||||||||||||||||||||
gtcagagtgtgagaccgatcgcctagctttaccgccattaatttgtccaaataaaaaaaagttccccactcgactgcaagagaaagtaagtattaacgggtctctcatggaatttgcagTGGCTACTCCGAAACAGATCAGGGAGGTGATGCAAGTGGACGGGCTTACAAACGATGAAGTGAAAAGCCATCTCCAG

upper sequence: LOC_Os03g55590.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G124540_T01 (Zea mays), 3'ss of exon 3
------gtatattacatggtcgaccatcattttcaccttccataatttgcaaagatcaccggaaatcctcatatcttgttgttccaccat-gattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG
       || |  |||  |  || | ||  |   |  ||   || |           |  ||| ||     | |       || |||| | | |||||||||||||||| ||||| |||||||||||||||||||| || ||||| || ||||| |||||||||||||||||||||
gtacatatacacgacaccgcggatcgtctgtaagaagtttactactagttgcttgctagaggagat----gtgttaacgaatttcaccgttggttgcagTTGCTACTCCGAAGCAGATCAGGGAGGTGATGAAGGTGGACGGGCTTACAAACGATGAAGTGAAAAGCCATCTCCAG

upper sequence: LOC_Os03g55590.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G33130.1 (Glycine max), 3'ss of exon 3
-------------gtatatt-acatggtcgaccatcattttcaccttccataatttgcaaagatcaccggaaatcctcatatcttgttgttccaccatgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG
             |||  || |  |||  |  ||| ||  | |  || ||   ||||    | |||   |   ||    ||   |  ||| |     | |||||||  ||||| ||||||||||| || ||| | ||| |||||||||| || || ||||| |||||||| |||||| | || 
tatctgtcaatctgtaagtttatttggaagggcatgataataaaattacacc-tttgtttggttcatttg---tctaattaaacttctgtgctgt--taattgcagCAGCTACACCAAAGCAAATTAGAGAGCTTATGCAGGTTGATGGCCTAACTAACGATGAAGTGAAGAGCCATTTACAA

upper sequence: LOC_Os03g55590.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S83_100V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatattacatggtcgaccatcatttt-cacctt-ccataatttgcaaagatcaccggaaatcctcatatcttgttgttccaccatgat---------tgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG
   | |  |   |||| |  ||   || ||  ||    |  | |  |      |   ||| | | || ||     |   |   || |           ||||||||| || |||||||||||  | ||| |||||||||| || || || ||||||||||||||||| |||||||| |||
---tttctctgtgtcggcattctccttgcattttgttctggtgtttatgttggattcgaacttcacaaattcaacttcactgacacgggctgtggttgtgcagTTGCCACGCCAAAGCAAATACGCGAGCTGATGAAGGTCGACGGCCTTACCAACGACGAAGTGAAGAGCCATCTGCAG

upper sequence: LOC_Os03g55590.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ37607 (Selaginella moellendorffii), 3'ss of exon 3
gtatattacatggtcgaccatcattttcaccttccataatttgcaaagatcaccggaaatcctcatatcttgttgttccaccatgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG
                              |  |  |||||          | |  || | || | |    |||  | |  | ||||  ||||||| ||||||||||||||| | ||| | |||||||| ||||| || || ||||| ||||| |||||||| ||||||
---------------------------gtgcgacagtaattcaagcgctcgatcaaaagttcttaaag---gtttcttcttcttgatc-cagTTGCAACTCCAAAGCAAATCCGAGAGCTCATGAAGGTAGATGGTCTTACAAACGATGAAGTAAAAAGCCACCTCCAG

upper sequence: LOC_Os03g55590.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ15083 (Selaginella moellendorffii), 3'ss of exon 3
gtatattacatggtcgaccatcattttcaccttccataatttgcaaagatcaccggaaatcctcatatcttgttgttccaccatgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG
           |  ||||  | ||| | |  ||| |    | |        | || || | || | |    |||  | |  | ||||  ||||||| ||||||||||||||| | ||  | |||||||| ||||| || || ||||| ||||| |||||||| ||||||
-----------gtgcgacagttattctgaa-ttcaagcgctcg--------atcgaaagttcttaaag---gtttcttcttcttgatc-cagTTGCCACTCCAAAGCAAATCCGAGAACTCATGAAGGTAGATGGTCTTACAAACGATGAAGTAAAAAGCCACCTCCAG

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|29673872|gb|CB670147.1|CB670147
EST:     GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
EST: gi|29668814|gb|CB665089.1|CB665089
EST:     CCGCCTTGCAGCAGCTCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: CCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
EST: gi|29668815|gb|CB665090.1|CB665090
EST:     GCCGCCTTGCAGCAGATCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: GCCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
EST: gi|58589449|gb|CF987757.1|CF987757
EST:     GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
EST: gi|29637019|gb|CB642028.1|CB642028
EST:     GCTTCCCCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
EST: gi|29641758|gb|CB646765.1|CB646765
EST:     GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
EST: gi|29668892|gb|CB665167.1|CB665167
EST:     CCGCCTTGCAGCAGCTCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: CCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
EST: gi|29675655|gb|CB671930.1|CB671930
EST:     AGTTCGTCGCCGCCTGGCAGCAGCTCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: AGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
EST: gi|29628391|gb|CB633402.1|CB633402
EST:     CGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: CGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
EST: gi|29644727|gb|CB649734.1|CB649734
EST:     GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
EST: gi|29639606|gb|CB644615.1|CB644615
EST:     GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
EST: gi|29669071|gb|CB665346.1|CB665346
EST:     GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
EST: gi|29674735|gb|CB671010.1|CB671010
EST:     GCTTCACCGGCAGTTTGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
EST: gi|29670047|gb|CB666322.1|CB666322
EST:     GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
EST: gi|29673933|gb|CB670208.1|CB670208
EST:     GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAG                         TTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA
genomic: GCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCA

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: 69 (upstream exon), 72 (downstream exon)
Score: 17

CAGCAGCAGCAGCAGCAGGCGAGGAAGTCGAGGCGGTGCTGGTCGCCGGAGCTTCACCGGCAGTTCGTCGCCGCCTTGCAGCAGCTCGGTGGCCCCCAAGgtatattaca ... atgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttgcaaagatcaccggaaatcctcatatcttgttgttccaccatgattgcagTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG
                           atatctt  TA-rich tract