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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG

Basic information

species Oryza sativa
transcript LOC_Os08g32620.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G119357_T01 (Zea mays), 3'ss of exon 2
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
                   || |    | | |    |  | || |||||  ||| |     |||  ||   ||   |  | ||||  ||    | ||      ||| || |   | ||  ||| ||| ||| || ||||| |||||||||||||||||||||||||| ||||||||||||||||| |  |||||||||||
-------------------gtacggagctcctcaatcctttcattgttgactttttc----ttctctg---tgcatgcgttttga--gcctgcttgtgataatttgggtgtgtgtatt--tttctctaaagGTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG

upper sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
                   ||      | | |   ||  | || || |||   ||| |  ||| |      |||       ||  | |||   | ||   || ||| ||| ||| |||    | ||| ||| || ||||| ||||||||||| |||||||| ||||| |||||||||||||||||||  |||||| ||||
-------------------gtatgaagctcctcaacccttccattgctgg--ctgtcccttttac------tgtgcatgcatttttagcttgcttgtga-tgattgggttgtctattt----tctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG

upper sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
gtatgcttgaatgctgattgttcatttcc-cgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
               |   ||| |||||    ||    ||||  ||  ||                 |  |   ||  |||| ||  |  || || ||   || ||  |||   ||||  | |||   |||| || |||||||| |||||||| || ||||| ||||| |||||||||||||| || |  |||||||| ||
---------------gtaagtttatttctgttttttttagtgagataatg--------------ttgtaagtgtttgaaatggtgggttttgttttgt---tgatttggttcggttttgtggttt---gaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG

upper sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G34740.3 (Glycine max), 3'ss of exon 2
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG-------------------------------
            |    || ||   || | |||    | ||  ||  |||  |||||    ||  | | |   ||  |||| ||  |  || || ||   || ||  ||||  ||||  |||||   |||| || |||||||| |||||||| || ||||| ||||| |||||||||||||| || |  |||||||| ||                               
------------gtaagtttttttatttctgttttt-actgagataatggtgttgtttgtgttttaagtgt--ttgaaatggtgggttttgttttgt---tgatttagtttggttttgtgtttt---gaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGGTAAAACCAGTATATTCTGCTTTTTTTTGTT

upper sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgttt---ttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
                              |||    | ||    | |||   | ||   |||    |   || | |    ||  ||     ||  ||| | ||||   ||| ||| | ||||   || ||||| || ||||| ||||||||||| || |||||||||||||||||||| || || || |  |||||||| ||
---------------------------gaggttattgattgtggggatggggattttgggttttg--gaactgatggggcttttctt-----tttttcttttcttgaactttttttgtggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG

upper sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
            |    || ||   || | |||    | ||  ||  |||  |||||    ||  | | |   ||  |||| ||  |  || || ||   || ||  ||||  ||||  |||||   |||| || |||||||| |||||||| || ||||| ||||| |||||||||||||| || |  |||||||| ||
------------gtaagtttttttatttctgttttt-actgagataatggtgttgtttgtgttttaagtgt--ttgaaatggtgggttttgttttgt---tgatttagtttggttttgtgtttt---gaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG

upper sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
               ||  | |  |||   | |  |  |  | | |  |    | ||   |||   |  |  |   |   |  |   |  |     | |  | |||||||||               |||| || ||||| ||||||||||| || |||||||||||||||||||| || || || |  |||||||| ||
--------------ggaggggt--ttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgtttt---------------gaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG

upper sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
                                |    ||   |||  |  ||  | |||    | | |   | |||  |  | || |    ||   | | |   |||  |   || ||  |  |||||||| |||||||| ||||| ||||| ||||| || || ||||||||||||||||| || | |||||| |||||
-------------------------------gtaagtagataaatagta-atcagatcagaa-ctacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttggttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG

upper sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
                                     |||   | ||||  |||| |  |||       |||| | ||||||  | || | ||||||       ||  |  | ||     || |  ||||| || ||||| || |||||||| || ||||| |||||||| ||||| |||||||| |  |||||||||||
----------------------------------gtgagtttga-gttgt-tttgctggattgatgattgatgattgaatgt--actggt-attcgtgggctgatgaatacttttgaattttgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG

upper sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S384_37V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
                                                         |  ||    |||||  |  |    ||   ||||     ||    |||  | |    | | |     |  | | ||     ||| |   ||   |||  |  | |  |   ||    |  | | ||    || || |||||||||||||||||||||||||| ||  |  | ||| || | ||| |    ||||| |||||
gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggcgttg---ggtcttctgtgaggtgcagtgagtcagggttaggt-ttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgtttc--agGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG

upper sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ05369 (Selaginella moellendorffii), 3'ss of exon 2
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggat-gttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaa---gATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
                                                                  |  ||| |  | |    | | |   |||||         ||   | | ||||| | ||| | |||   | ||||||||||| |||||||| ||||||||||||||||| ||||||||||| || || ||||| |||||
-----------------------------------------------------------------gtaagattgacaaagctctcactttggattctctatcttatgctctctttttttgggtttgcggaaacagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG

upper sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttc--tgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
                                  | |  ||   |      | | ||   | ||   |    |||   ||    | | ||  ||| |||||  |  | ||  |     | || ||   ||||| || ||||| ||||||||||||||||| ||||| ||| | ||||| ||||||||   ||||||||| ||
--------------------------------gtctcgttgtgttcgaacttctctttcctctcttggtctcgttgtgat-cgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG

upper sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ17782 (Selaginella moellendorffii), 3'ss of exon 2
----------------------------------gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatggga-------tgttagaatgttgattgctgattcgtctctgcttgtgttttcttttt---cgtttttct----gaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
                                  || |  |||| |  |  | |||| | ||  | | | |  |    | ||||  | |||   ||   || | |       ||||    |  || | |    |   | ||| ||  ||| |||||      || |||  |    |||| || ||||||||||||||||||||||| ||||| ||| | ||||| ||||||||   ||||||||| ||
gtaagtgctctctctctccctctgtctctctggcgtctcgttgactagttgt-gttcttatcaagcttctctttcttctcttggtctcgttgtgttcttatcgaacttctcctgttctcgttgtgttcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG

upper sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ26805 (Selaginella moellendorffii), 3'ss of exon 2
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggat-gttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
                                                                  |  ||| |  | |    | | |   |||||         ||   | | ||||| | |||     || ||||||||||| |||||||| ||||||||||||||||| ||||||||||| || || ||||| |||||
-----------------------------------------------------------------gtaagattgacaaagctctcactttggattctctatcttatgctctctttttttgggtttgaaacagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG

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|33801423|gb|CF326583.1|CF326583
EST:     TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGT                         ATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTG
genomic: TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGTgtatgcttga ... ttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTG
EST: gi|88478431|gb|CI415702.1|CI415702
EST:     TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGT                         ATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTG
genomic: TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGTgtatgcttga ... ttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTG
EST: gi|88485934|gb|CI423205.1|CI423205
EST:     TACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGT                         ATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTG
genomic: TACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGTgtatgcttga ... ttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTG
EST: gi|88845520|gb|CI084445.1|CI084445
EST:     TTCGAGTACAAGGCCGCNACCGGCGCCTTCACCCCCGACCGCGTCGCCGT                         ATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTG
genomic: TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGTgtatgcttga ... ttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTG
EST: gi|88508474|gb|CI435980.1|CI435980
EST:     TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGT                         ATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTG
genomic: TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGTgtatgcttga ... ttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTG
EST: gi|86508991|gb|CI151624.1|CI151624
EST:     TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGT                         ATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTG
genomic: TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGTgtatgcttga ... ttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
          tgctgat  putative branch site (score: 3)
                ttcgtctctgcttgtg  CT-rich tract
                                ttttcttttt  TA-rich tract