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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgccaggaatatttgaacatacatataataactgacatacctcctttgtctgtgatatgactcactgtttttttcccctcctattttcatatttgtgaagTTCAAAGCGTTTCACGTATGATGATGTTGTTGAAAAAGTTGCTAATCAACTTGGACTCGATGATCCTTCCAAACTCCGCCTTACACAACACCTCCCGTAT

Basic information

species Oryza sativa
transcript LOC_Os01g56490.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 22
lower sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 21
gtatgtgccaggaa-----tatttgaacatacatataataactgacatacc--------tcctttgtctgtgatatgactcactgtttttt--------tcccctcctattttcatattt--gtgaagTTCAAAGCGTTTCACGTATGATGATGTTGTTGAAAAAGTTGCTAATCAACTTGGACTCGATGATCCTTCCAAACTCCGCCTTACACAACACCTCCCGTAT
||| ||  |||        || |      || ||   ||  |  |  || |        |    | ||  ||       | | |   ||||        |    |   |   |||| ||    || || |||||||    ||||||||||||||| || ||||||||||||||  | || |||||||| |||||||| |||||  | || ||   |||   |   || 
gtaagtatcagagcaactctactcaggtgtaaatcccatcgcatatgtatcagtgtttgtttcatatccttgccgaatttaaatagattttggagagtattgtttttcaagatcatgttgcaatgcagATCAAAGCAACACACGTATGATGATGTAGTAGAAAAAGTTGCTAAGAAGCTCGGACTCGAGGATCCTTCAAAACTTAGGCTCACGTCACATAACTGTTAC
















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|58694066|gb|CK082753.1|CK082753
EST:     CACTTCAGATTACTTGAGAATCCAAAAGATGATGACTTCACTTTGGAGCT                         TTCAAAGCGTTTCACGTATGATGATGTTGTTGAGAAAGTTGCTAATCAACT
genomic: CACTTCAGATTACTTGAGAATCCAAAAGATGATGACTTCACTTTGGAGCTgtatgtgcca ... atttgtgaagTTCAAAGCGTTTCACGTATGATGATGTTGTTGAAAAAGTTGCTAATCAACT
EST: gi|58679445|gb|CK068132.1|CK068132
EST:     CACTTCAGATTACTTGAGAATCCAAAAGATGATGACTTCACTTTGGAGCT                         TTCAAAGCGTTTCACGTATGATGATGTTGTTGAGAAAGTTGCTAATCAACT
genomic: CACTTCAGATTACTTGAGAATCCAAAAGATGATGACTTCACTTTGGAGCTgtatgtgcca ... atttgtgaagTTCAAAGCGTTTCACGTATGATGATGTTGTTGAAAAAGTTGCTAATCAACT
EST: gi|44670906|gb|CR284340.1|CR284340
EST:     CACTTCAGATTACTTGAGAATCCAAAAGATGATGACTTCACTTTGGAGCT                         TTCAAAGCGTTTCACGTATGATGATGTTGTTGAGAAAGTTGCTAATCAACT
genomic: CACTTCAGATTACTTGAGAATCCAAAAGATGATGACTTCACTTTGGAGCTgtatgtgcca ... atttgtgaagTTCAAAGCGTTTCACGTATGATGATGTTGTTGAAAAAGTTGCTAATCAACT
EST: gi|58656896|gb|CK045576.1|CK045576
EST:     CACGTGGGATTACTTGAGAATCCAAAAGATGATGACTTCACTTTGGAGCT                         TTCAAAGCGTTTCACGTATGATGATGTTGTTGAGAAAGTTGCTAATCAACT
genomic: CACTTCAGATTACTTGAGAATCCAAAAGATGATGACTTCACTTTGGAGCTgtatgtgcca ... atttgtgaagTTCAAAGCGTTTCACGTATGATGATGTTGTTGAAAAAGTTGCTAATCAACT

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: 58 (upstream exon), 68 (downstream exon)
Score: 12

GTTGTCCACTTCAGATTACTTGAGAATCCAAAAGATGATGACTTCACTTTGGAGCTgtatgtgcca ... atttgtgaagTTCAAAGCGTTTCACGTATGATGATGTTGTTGAAAAAGTTGCTAATCAACTTGGACTCGATGATCCTTCCAAACTCCGCCTTACACAACACCTCCCGTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtctgtgatatgactcactgtttttttcccctcctattttcatatttgtgaagTTCAAAGCGTTTCACGTATGATGATGTTGTTGAAAAAGTTGCTAATCAACTTGGACTCGATGATCCTTCCAAACTCCGCCTTACACAACACCTCCCGTAT
             gactcac  putative branch site (score: 12)
               ctcactgtttttttcc  CT-rich tract
                                    tattttcatatttgt  TA-rich tract