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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacaagtacagaaccattatgttaagcaatactttattactctcagaatagtgattttgcagttgttttgtgcgataacataatttttttctgctgtcagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g16970.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16970.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AC213600.3_FGT002 (Zea mays), 3'ss of exon 12
tacaagtacagaaccattatgtta-agcaatactttattactctcagaatagtgattttgcagttgtt-ttgtgcgataacataatttttttctgctgtcagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAG
|  |   |  | |      || || |  ||     |   |   || | ||  |  ||   ||    |  || ||| |||| |  | |||   ||    ||||||| ||||||||||||||||| || |||||||| ||||| ||||||| |||||||| |||||||||||| ||||||||||| ||||||
tttagaaagtggatttcagtgatagaataacttgcttgaatgttcggtatgttttttccccacacatccttatgccataaaacgaatttc--ctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG

upper sequence: LOC_Os01g16970.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G052875_T02 (Zea mays), 3'ss of exon 12
tacaagtacagaac-cattatgttaagcaatactttatt---actctcagaatagtgattttgcagttgttttg-tgcgataacataatttttttctgctgtcagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAG
   |  || | |   ||||  || |   |||   ||  |   |  ||  | ||  |  || | ||  |||  ||  ||  ||| |  | ||||  ||    ||||| | |||||||||||||||||||| |||||||||||||| ||||||  |||||||| |||||||||||| ||||||||||| ||||||
---acttagaaactgcattcagtgatagaatgacttgcttgaatgcttggcatgttttttgttcacatgtcctgacgccttaaaacgaatttt--ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG

upper sequence: LOC_Os01g16970.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA20G02950.2 (Glycine max), 3'ss of exon 10
---------------------------------------------tacaagtacagaaccattatgttaag--caatactttattactctcagaatagtgattttgcagttgttttgtgcg-----ataacataatttttttctgct-gtcagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAG
                                                 |||| | |   | ||    |||  |||   |  |||  |   |  | |||  | || |      | |          ||||   |||||  ||||  |   |||| |||||||||||||||| || || ||||||||||||   ||||| ||||| || | |||||||||||| || ||  | ||| | |||
gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaataaaataaaaaaagtgcaagcgtcaattggtggaaacaaagttctatttccccccctctaaaaaggtaaataattcaatttccttctttttaacagGAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAG

upper sequence: LOC_Os01g16970.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA07G35090.1 (Glycine max), 3'ss of exon 13
--------------------------------tacaagtacagaaccattatgttaagcaatac-----tttattactctcagaatagtgattttgcagttgttttgtgcg----ataacataatttttttctgctgt-cagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAG
                                |    || |    |     | | ||  | | |     |  |||  |   |  | |||  | || |     | |     |    ||||    ||||  ||||  | | |||| |||||||||||||||| || || ||||||||||||   ||||| ||||| || | |||||||||||| |||||  | ||| | |||
gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaaaaagtgcaagcgtcaattggtgaaaacaaagttctatttcccccctctaaaaaggcaaataattcgatttccttcttttttacagGAGCTGGGACAAATTTGAGGATTCATACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCTGATAGGAGTTTGAAG

upper sequence: LOC_Os01g16970.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv06s0004g00140.t01 (Vitis vinifera), 3'ss of exon 12
-------tacaagtacagaaccattatgttaagcaatactttattactctcagaatagtgattttgcagttgttttgtgcgataacataatttttttctgctgtcagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAG
       |     ||||    | || | || |    | | |  || || ||    |  ||||||     ||  |  |     |       |  || |||||    ||||||||||| ||||||||||| || ||||||   ||||  ||||||||||| || | |||||||||||| |||||  | ||| | |||
gacctgtttttcctacatg-tctttttcttgaaagttgcatgttttctttc---gtcttgattt---gcttactgagcattttctttctttcattatctgcaaatagGCGCTGGGATAAATTTGAAGATTCATACAGAACTATGCTGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAG

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|38481101|gb|CF965190.1|CF965190
EST:     CCATTCAAGAAAGCTTCGCAGGTTGAAGGACATAGTACCACCAGCCTGGG                         GCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGG
genomic: CCATTCAAGAAAGCTTCGCAGGTTGAAGGACATAGTACCACCAGCCTGGGgtatgtttgt ... ctgctgtcagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGG
EST: gi|88371457|gb|CI602635.1|CI602635
EST:     CCATTCAAGAAAGCTTCGCAGGTTGAAGGACATAGTACCACCAGCCTGGG                         GCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGG
genomic: CCATTCAAGAAAGCTTCGCAGGTTGAAGGACATAGTACCACCAGCCTGGGgtatgtttgt ... ctgctgtcagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGG
EST: gi|58589761|gb|CF988069.1|CF988069
EST:     CCATTCAAGAAAGCTTCGCAGGTTGAAGGACATAGTACCACCAGCCTGGG                         GCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCA
genomic: CCATTCAAGAAAGCTTCGCAGGTTGAAGGACATAGTACCACCAGCCTGGGgtatgtttgt ... ctgctgtcagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatagtgattttgcagttgttttgtgcgataacataatttttttctgctgtcagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAG
                           cgataac  putative branch site (score: 3)
                                      tttttttctgctgtc  putative PPT
                             ataacataattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacaagtacagaaccattatgttaagcaatactttattactctcagaatagtgattttgcagttgttttgtgcgataacataatttttttctgctgtcagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA