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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgagcgcgcttcatgtattcctggttctttcgttttggacaggaattgttgttgaagctaaggaaggcagcatctcacattatttcgatccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCG

Basic information

species Oryza sativa
transcript LOC_Os03g18070.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G074401_T01 (Zea mays), 3'ss of exon 2
gtaagatgagcgcgcttcatgtattcctggttctttcgttttggacaggaattgttgttgaagctaaggaaggcagcatctcacattatttcgatccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCG
      |  |    |  ||||| |  |  | |  || ||||  | |  | ||| | ||||| |  | ||||     || ||  | ||   |    ||| |||||||||||||||||||||||||||||| || |||||||| || || ||||| |||||||||||||| |||
-----gtaggattaccccatgtttctcatgcttgttagtttctgtcgaggattatcgttgatgtcatggaa----ccacctgcctttgaatg---ccattttcagGAGGATTAGCCACAGGACGCACCATCAAAACCACGGCCACGTTGAGAAGGACGAGTCCTGGCACCCG

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G128971_T01 (Zea mays), 3'ss of exon 2
gtaagatgagcgcgcttcatgtattcctggttctttcgttttggacaggaattgttgttgaagctaaggaaggcagcatctcacattatttcgatccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCG
||| ||| | |      ||||| | |   | || || ||||  | |  | ||  | ||||| | |                     ||  |  ||  |||||||||||||||||||||||||||||||| || ||||||||||| || ||||| |||||||||||||| |||
gtaggattacc------catgtttcctatgctcgttagtttctgtcgaggatcatcgttgatgttg--------------------taagtgaatggaatttcagGAGGATTAGCCACAGGACGCACCATCAAAACCACGGTCACGTTGAGAAGGACGAGTCCTGGCACCCG

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G11170.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagatgagcgcgcttcatgtattcctggttctttcgttttggacaggaattgttgttgaagctaaggaaggcagcatctcacattatttcgatccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCG
         | | | ||    |  |    |  | ||| | |     |  |    |||  ||| || |      |  | ||    |  | |  ||     || |||||| ||||| ||||| || |||||||||||||| || ||||| ||||| ||||| || ||||| || 
---------gtgagttt----tgctttcagaccattcttctc---taaaaccacttgcagaatctcat-----cttcttcatgtaaaaatatgact---ttgcagGAGAATTAGTCACAGAACTCACCACCAGAACCATGGACATGTTGAGAATGACGAATCTTGGCATCCT

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
-------gtaagatgagcgcgcttcatgtattcctggttctttcgttttggacag-gaattgttgttgaagctaaggaaggcagcatctcacattatttcgatccaattt-cagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCG
        |    | |   |  |  || || | |      ||||  | | |  |  ||||   |     |   |    |         | ||| |||||  ||     ||  ||||||||||||||||| || |||||||||||||| |||||||||||||| ||||| || ||||| || 
gtgacttttgctttcaatcccttcaatataatacaaaccttttctctcttggtaatgaatcacttgaagaataatatcacattcttcatgacaatatttgaattttccttgtagGAGGATTAGCCACAGAACTCACCACCAGAACCATGGTCATGTCGAGAATGACGAATCATGGCATCCT

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S98_209V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagatgagcgcgctt-catgtattcctggttctttcgttttggacaggaattgttgttgaagctaaggaaggcagcatctcacattatttcgatccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCG
|| ||| |    | | | |   | ||| | || ||   |||   |||    |||||  |   ||||     ||     |    |  || |   |         |||| | |||||||||||||| ||||||||||||||||| || || ||||| |||||||| ||||| || 
gtgagaagctttcacgtgcccttcttcatcgtgctgaagttaatgacgtacattgtattc--agctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S65_6V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagatgagcgcgcttcatgtattcctggttctttcgttttgga-caggaattgtt--gttgaagcta--aggaaggcagcatctcacat-tatttcgatccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCG
      ||||     |||   || |      || ||||| |||||  ||    ||||      | || |   | |  |  |   || |  | | |   |       | |||| ||||||||||||| || |||||||||||||| || ||||| ||||| |||||||| ||||| |||
-----gtgagaatctttctcataatgtc--ctccttcgtcttggagtagatgctgtttcacacatgccattggtagagttgtgactgaattgtgtgatggggtgggtgcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ23113 (Selaginella moellendorffii), 3'ss of exon 2
gtaagatgagcgcgcttcatgtattcctggttctttcgttttggacaggaattgttgttgaagctaaggaaggcagcatctcacattatttcgatccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCG
                             || | |  | |||       | || |||||     ||  |          || | | | | | ||    | | ||||||||| |||||| ||||||| |||||||| ||||| ||||||||||| |||||||||||||| || 
-----------------------------gtacgtatgcttttc----catttcttgtttggcttagag----------cttaaactttgtgga----aatccagGAGGATAAGCCACCGGACGCATCACCAGAATCACGGCCATGTCGAGAACGACGAGTCCTGGCATCCA

upper sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ20170 (Selaginella moellendorffii), 3'ss of exon 2
gtaagatgagcgcgcttcatgtattcctggttctttcgttttggacaggaattgttgttgaagctaaggaaggcagcatctcacattatttcgatccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCG
                             || | |  | |||       | || |||||     ||  |           | | | | | | ||    | | ||||||||| |||||| ||||||| |||||||| ||||| ||||||||||| |||||||||||||| || 
-----------------------------gtacgtatgcttttc----catttcttgtttggcttagag----------tttaaactttgtgga----aatccagGAGGATAAGCCACCGGACGCATCACCAGAATCACGGCCATGTCGAGAACGACGAGTCCTGGCATCCA

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|88691310|gb|CI733894.1|CI733894
EST:     GTGGTTGGACACATACTCCACTCCTCCATCCTTGTCCCATACCACGGCTG                         GAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGA
genomic: GTGGTTGGACACATACTCCACTCCTCCATCCTTGTCCCATACCACGGCTGgtaagatgag ... ccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGA
EST: gi|58587962|gb|CF986270.1|CF986270
EST:     GTGGTTGGACACATACTCCACTCCTCCATCCTTGTCCCATACCACGGCTG                         GAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCACGTCGAGAAAGA
genomic: GTGGTTGGACACATACTCCACTCCTCCATCCTTGTCCCATACCACGGCTGgtaagatgag ... ccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGA
EST: gi|88688814|gb|CI732390.1|CI732390
EST:     GTGGTTGGACACATACTCCACTCCTCCATCCTTGTCCCATACCACGGCTG                         GAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGA
genomic: GTGGTTGGACACATACTCCACTCCTCCATCCTTGTCCCATACCACGGCTGgtaagatgag ... ccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGA
EST: gi|88689151|gb|CI732727.1|CI732727
EST:     GTGGTTGGACACATACTCCACTCCTCCATCCTTGTCCCATACCACGGCTG                         GAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGA
genomic: GTGGTTGGACACATACTCCACTCCTCCATCCTTGTCCCATACCACGGCTGgtaagatgag ... ccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGA
EST: gi|88691186|gb|CI735265.1|CI735265
EST:     GTGGTTGGACACATACTCCACTCCTCCATCCTTGTCCCATACCACGGCTG                         GAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGA
genomic: GTGGTTGGACACATACTCCACTCCTCCATCCTTGTCCCATACCACGGCTGgtaagatgag ... ccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGA

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), 68 (downstream exon)
Score: 63

TGGCCATGGGAGCTTCTCAAGCAACGCCAAGTTGAACAGCGTGGTTGGACACATACTCCACTCCTCCATCCTTGTCCCATACCACGGCTGgtaagatgag ... ccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttgttgaagctaaggaaggcagcatctcacattatttcgatccaatttcagGAGGATTAGCCACAGGACGCACCACCAGAACCACGGTCATGTCGAGAAAGACGAGTCCTGGCAACCG
                           atctcac  putative branch site (score: 63)
                                acattattt  TA-rich tract