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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggactaggtaatttttatttttatttaaaactactaaatatgttaatatcgcacacatcacaagcaggcaactttaggatactcttttttggccttgcagGTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCAACAAAGCATATGCCTACACCTGAACAATGGACCAATGTCTTCAACCCAG

Basic information

species Oryza sativa
transcript LOC_Os05g28180.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 12
ggactaggtaattt--ttatttttatttaaaactac-taaatatgttaatatcgcacacatcacaagcaggcaactttaggatactcttttttggccttgcagGTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCAACAAAGCATATGCCTACACCTGAACAATGGACCAATGTCTTCAACCCAG
  | ||| |  ||   | ||  | ||| | || ||| |    ||||   |||| || | | ||  |     |||||| |    ||||||| | ||||||||||||||||||||| ||  ||||||||||||| |||||||| |||||||||||||||||||| ||||| ||||||||||| ||||||||||| |||||||| |
--attagttttttcagtaatgataattgagaaatacgttcgcatgtatttatctcagata-catgatatcacaacttcaattgactctttctgggccttgcagGTTGTAGGGTTGGACCTGGTTGATGATGAAAGTAAACCAGAAAGGCGTCCAACAAAGCACATGCCCACACCTGAACAGTGGACCAATGTGTTCAACCCTG

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 13
-----ggactaggtaatttttatttttatttaaaacta--ctaaatatgttaatatcgcacacatcacaagcaggcaactttaggatactcttttttggccttgcagGTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCAACAAAGCATATGCCTACACCTGAACAATGGACCAATGTCTTCAACCCAG
      |   ||  ||   | ||| || ||  ||| ||  || ||   |  | ||||  |    |||  |          |||      |  | |      ||  ||||||| ||||| ||||||||||||||||| || ||||||||||| || |||||||| || |||||||||||||| |||||||| ||||| ||||| || |
cacaaagctcagaaaaaaataattatttttctaaaataagctgaaccagacattatcttat--ttcagtactgtatggtattaa-----ttctctacacttttttagGTTGTTGGGTTGGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCGG

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 12
ggactaggtaatttttatttttatttaaaactactaaatatgttaatatcgcacacatcacaagcaggcaactttaggatact--cttttttggccttgcagGTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCAACAAAGCATATGCCTACACCTGAACAATGGACCAATGTCTTCAACCCAG
  || | || |     |       |||    |   ||||| ||| | | |  ||| |     |       ||| || | || |   || ||     ||  ||||||| ||||| |||||||| |||||||| || ||||||||||| || |||||||| || ||||||||||| || |||||||| ||||| ||||| ||||
-cacaaagtcaaagaaaaaagccattatttttctaaaataagttga-accagacatactcttattccagtactgtatggtattaatttcttcacttttttagGTTGTTGGGTTGGATTTGGTGGATGATGAAAGCAAACCTGAAAGACGGCCAACAAAACACATGCCTACACCGGAGCAATGGACTAATGTATTCAATCCAG

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 12
ggactaggtaatttttatttttatttaaaactactaaatatgttaatatcgcacacatcacaagcaggc--aactttaggata-ctcttttttggccttgcagGTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCAACAAAGCATATGCCTACACCTGAACAATGGACCAATGTCTTCAACCCAG
      | ||   || || | |    | |||  ||||      |    |  |||| || |  ||  ||    |||    | |  ||||| ||||   || |||||||| || || ||||||||||||||||| || ||||||||||| ||||| ||||| || ||||| || || |  |||||||| || |  ||||| || |
------gttagcattcatatcttcaaataacctctaatccgcatgtctttacaca-ataaagagttggtttgactggttgctgtctcttgtttgctatttcagGTTGTTGGATTTGATTTGGTTGATGATGAAAGCAAACCTGAAAGACGTCCCACAAAACACATGCCCACTCCAGCTCAATGGACTAACGCATTCAATCCTG

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S307_76V6.1 (Physcomitrella patens), 3'ss of exon 12
ggactaggtaatttttatttttatttaaaactactaaatatgttaata-------tcgcacacatcacaagcaggcaactttaggatactcttttttg-gccttgcagGTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCAACAAAGCATATGCCTACACCTGAACAATGGACCAATGTCTTCAACCCAG
     |  | |   ||  | | |  ||||| |||    |   |||  |       | |  ||  |       |     |||||    |||||||  || |    |||||| |||||||| ||| |||| |||||||||||||| ||||||||| | || ||||| || ||||  || |||| | |||||| |||   |||||||||||
----aatatcacaattgatataaagtaaaattacagtcttcattagcaaggagatttgttcatgttctttttaatttgcttta----actctttggtgtggggggcagGTGGTAGGGTTTGATATGGTGGATGATGAGAGTAAGCCTGAAAGGAGGCCCACAAAACACATGCAGACTCCTGCAGAATGGAACAACCCCTTCAACCCAG

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------------------------------------------------ggactaggtaatttttatttttatttaaaactactaaatatgttaatatcgcacacatcacaagcagg---caa-----ctttaggatactcttttttggccttgcagGTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCAACAAAGCATATGCCTACACCTGAACAATGGACCAATGTCTTCAACCCAG
                                                                       ||| | ||   |||  |||| |     | |  |  | ||      ||      | |  | |   ||   |||     ||||     | | ||| ||        ||||||| || || ||| |||| ||||||||||| || ||||||||||| ||||| ||||| ||||   ||||||   |||||   |||   ||||| ||||
gttggtcaaaagcaaaaccaaacccccagcgtcatgcgtcttttcgtttacattcttgtccgctttctccaactggatacgatttgcttttgtcgcgtattggtcgaaataacctgataatttgctttcccattgggtttcaatccttctttcatgcattttttgttaaatgaatagGTTGTTGGATTCGATATGGTGGATGATGAGAGCAAGCCTGAAAGGCGGCCAACGAAGCACATGCAACCACCTGCGAAATGGGATAATCCTTTCAATCCAG

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|58687285|gb|CK075972.1|CK075972
EST:     TCACCATTGATCCAGCTTCTCATCCGCAGCTTCACGTCTTCCTAAAGCAG                         GTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCA
genomic: TCACCATTGATCCAGCTTCTCATCCGCAGCTTCACGTCTTCCTAAAGCAGgttcaatagt ... ggccttgcagGTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCA
EST: gi|33796571|gb|CF324153.1|CF324153
EST:     TCACCATTGATCCAGCTTCTCATCCGCAGCTTCACGTCTTCCTAAAGCAG                         GTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCA
genomic: TCACCATTGATCCAGCTTCTCATCCGCAGCTTCACGTCTTCCTAAAGCAGgttcaatagt ... ggccttgcagGTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCA
EST: gi|88693457|gb|CI737032.1|CI737032
EST:     TCACCATTGATCCAGCTTCTCATCCGCAGCTTCACGTCTTCCTAAAGCAG                         GTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCA
genomic: TCACCATTGATCCAGCTTCTCATCCGCAGCTTCACGTCTTCCTAAAGCAGgttcaatagt ... ggccttgcagGTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcgcacacatcacaagcaggcaactttaggatactcttttttggccttgcagGTTGTAGGGTTAGATTTGGTTGATGATGAGAGTAAACCTGAAAGGCGTCCAACAAAGCATATGCCTACACCTGAACAATGGACCAATGTCTTCAACCCAG
 tgttaat  putative branch site (score: 3)
                                    ctcttttttggcctt  putative PPT
                                     tctttttt  TA-rich tract