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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtcaacagtcacagtgatttaatttactaatagtgttaactaggaaccatttgctaaagctaaccatcccccatgggttttcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAACACCAAAGTGGTAGTTGAGTCTGGTGCTGTGCCCATCTTTGTCAAACTGC

Basic information

species Oryza sativa
transcript LOC_Os05g06350.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06350.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G088088_T01 (Zea mays), 3'ss of exon 3
gtgtgtcaacagtcacagtgatttaatttactaatagtgttaactaggaaccatttgctaaa-gctaaccatcccccatgggt--tttcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAACACCAAAGTGGTAGTTGAGTCTGGTGCTGTGCCCATCTTTGTCAAACTGC
|| ||  ||||||  || ||||  | | ||    |    || | |      |  ||  |||  | |  | ||   | ||   |   || |   ||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| || ||||| ||||||  |||||||||||||||||||||||| || |
gtctgggaacagtagcactgatcaattatatggttttactttattttc--tctcttattaatcggtggcaatttgcgatatataacttatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTGGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC

upper sequence: LOC_Os05g06350.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G468150_T01 (Zea mays), 3'ss of exon 2
gtgtgtcaacagtcacagtgatttaatttactaatagtgttaactaggaaccatttgctaaa-gctaaccatcccccatgggt--tttcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAACACCAAAGTGGTAGTTGAGTCTGGTGCTGTGCCCATCTTTGTCAAACTGC
|| ||  ||||||  || |||   | | ||    |    || | |      |  ||  |||  | |  | ||   | ||   |   || |   ||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| || ||||| ||||||  |||||||||||||||||||||||| || |
gtctgggaacagtagcactgaacaattatatggttttactttattttc--tctcttattaatcggtggcaatttgcgatatataacttatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTCGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC

upper sequence: LOC_Os05g06350.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G086022_T02 (Zea mays), 3'ss of exon 1
gtgtgtcaacagtcacagtgatttaatttactaatagtgttaactaggaaccatttgctaaa-gctaaccatcccccatgggt--tttcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAACACCAAAGTGGTAGTTGAGTCTGGTGCTGTGCCCATCTTTGTCAAACTGC
|| ||  ||||||  || ||||  | | ||    |    || | |      |  ||  |||  | |  | || | | ||   |   || |   ||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| || ||||| ||||||  |||||||||||||||||||||||| || |
gtctgggaacagtagcactgatcaattatatggttttactttattttc--tctcttattaatcggtggcaattcgcgatatataacttatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTGGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC

upper sequence: LOC_Os05g06350.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G009845_T02 (Zea mays), 3'ss of exon 3
gtgtgtcaacagtcacagtgatttaatttactaatagtgttaactaggaaccatttgctaaa-gctaaccatcccccatgggt--tttcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAACACCAAAGTGGTAGTTGAGTCTGGTGCTGTGCCCATCTTTGTCAAACTGC
|| ||  |||| |||   ||||  |    |    |    || | |    | |  ||  |||    || | |    | ||  ||    | |   ||||||||||||||||||||| ||||| ||||||||||||||||||||||| ||||| || ||||| ||||||  ||||||||||||||||||||| || || |
gtttgggaacactcatcctgatcaatcacatggctttacttcattt--tatctcttattaatcagtagcaacttgctatatgtaacatatgctgcagTTTGAGGCTGCATGGGCGCTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTGGTTGAGAGTGGTGCTGTGCCCATCTTTGTTAAGCTCC

upper sequence: LOC_Os05g06350.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S43_141V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------gtgtgtcaacagtcacagtgatttaatttactaatagtgttaactaggaaccatttgctaaagctaaccatcccccatgggttttcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAACACCAAAGTGGTAGTTGAGTCTGGTGCTGTGCCCATCTTTGTCAAACTGC
                    ||        | || |    || |||| || ||       | |  |     |  |  | | | | | || | ||| |  |  | | ||||||||||||| ||||||||  | |||||||||||||| || ||||| ||| ||||    || ||  |||||  ||| ||||| || ||||||||  | || |
gtacctgtctgtgttacccctgctgttgacctcattagaatagtttattattaagccctgcgacaagagggtgac--atgatgatc-tcacacattgaatggccttcgcagTTTGAGGCAGCATGGGCGTTGACTAACATTGCATCCGGAACATCTGATCACACTCGTGTTGTGATTGAGCATGGGGCTGTTCCTATCTTTGTTCAGCTTC

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|38565792|gb|CK085245.1|CK085245
EST:     ATTATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAAC
genomic: ATTATCCCCAACTCCAGgtgtgtcaac ... tcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAAC
EST: gi|66925025|gb|CX111873.1|CX111873
EST:     TGCCTCGCTTTATTGCCTTCCTCCAACGTGAGGATTATCCCCAACTCCAG                         TTTGAGGCTGGATGGGCACTCACTAACATTGGATCAAGCACATCAGATAAC
genomic: TGCCTCGCTTTATTGCCTTCCTCCAACGTGAGGATTATCCCCAACTCCAGgtgtgtcaac ... tcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAAC
EST: gi|33793316|gb|CF322538.1|CF322538
EST:     TGCCTCGCTTTATTGCCTTCCTCCAACGTGAGGATTATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAAC
genomic: TGCCTCGCTTTATTGCCTTCCTCCAACGTGAGGATTATCCCCAACTCCAGgtgtgtcaac ... tcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAAC
EST: gi|33797470|gb|CF324595.1|CF324595
EST:     TGCCTCGCTTTATTGCCTTCCTCCAACGTGAGGATTATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAAC
genomic: TGCCTCGCTTTATTGCCTTCCTCCAACGTGAGGATTATCCCCAACTCCAGgtgtgtcaac ... tcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAAC
EST: gi|58664150|gb|CK052836.1|CK052836
EST:     TGCCTCGCTTTATTGCCTTCCTCCAACGTGAGGATTATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAAC
genomic: TGCCTCGCTTTATTGCCTTCCTCCAACGTGAGGATTATCCCCAACTCCAGgtgtgtcaac ... tcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAAC
EST: gi|58653933|gb|CK042613.1|CK042613
EST:     GCCTCGCTTTATTGCCTTCCTCCAACGTGAGGATTATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAAC
genomic: GCCTCGCTTTATTGCCTTCCTCCAACGTGAGGATTATCCCCAACTCCAGgtgtgtcaac ... tcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAAC

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: 74 (upstream exon), 75 (downstream exon)
Score: 141

AGCGGAGTCCTCCAATTGAGGAGGTGATCAACACAGGGGTGGTGCCTCGCTTTATTGCCTTCCTCCAACGTGAGGATTATCCCCAACTCCAGgtgtgtcaac ... tcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAACACCAAAGTGGTAGTTGAGTCTGGTGCTGTGCCCATCTTTGTCAAACTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaactaggaaccatttgctaaagctaaccatcccccatgggttttcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAACACCAAAGTGGTAGTTGAGTCTGGTGCTGTGCCCATCTTTGTCAAACTGC
                      agctaac  putative branch site (score: 141)
                                          ttttcttgc  putative PPT
                                          ttttctt  TA-rich tract