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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agacctggcaaaaacttggtaaaatagctgtatattcagtgattccattgtgctaggttaatctactcttgataatcatggactgattttgtgtatgcagTGGATTGCATTGATTGTGCAGCAGACGCATCTGTGGTGGGTGCAGTGAATGAAGGTATTGATGTAGCAGCCTCAATTGTGCCAGCAGTTCAAAGGCCATG

Basic information

species Oryza sativa
transcript LOC_Os05g06510.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06510.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G864166_T01 (Zea mays), 3'ss of exon 2
----agacctggcaaaaacttggtaaaatag--ctgtatattcagtgattccattgtgctaggttaatctactcttgataatcatggactgattttgtgtatgcagTGGATTGCATTGATTGTGCAGCAGACGCATCTGTGGTGGGTGCAGTGAATGAAGGTATTGATGTAGCAGCCTCAATTGTGCCAGCAGTTCAAAGGCCATG
          | ||||| ||     ||| ||  |  || | | |   ||| ||   ||  | ||||   ||| |||   ||| |||| |  ||| |||  ||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||| |||||||| ||| ||||||||||||| ||
gcttttggtggccaaaagctgaaacaaacagggccatacacttatgaattgcaacttg--atgtta---tacacttacgaattatgggc-aattctgtacatgcagTGGATTGCATTGATTGTGCAGCAGATGCATCTGTGGTGGGAGCAGTGAATGAAGGTATTGAAGTAGCAGCATCAATTGTACCAACAGTTCAAAGGCCTTG
















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|88762903|gb|CI772459.1|CI772459
EST:     GATGCTGCCGATGTCAGGAATCTCTCCCTTGTATACACGCTTGCCGGAG                         TGGATTGCATTGATTGTGCAGCAGACGCATCTGTGGTGGGTGCAGTGAATG
genomic: GATGCTGCCGATGTCAGGAATCTCTCCCTTGTATACACGCTTGCCGGAGgtatgcttgt ... gtgtatgcagTGGATTGCATTGATTGTGCAGCAGACGCATCTGTGGTGGGTGCAGTGAATG
EST: gi|58671815|gb|CK060501.1|CK060501
EST:     GATGCTGCCGATGTCAGGAATCTCTCCCTTGTATACACGCTTGCCGGAG                         TGGATTGCATTGATTGTGCAGCAGACGCATCTGTGGTGGGTGCAGTGAATG
genomic: GATGCTGCCGATGTCAGGAATCTCTCCCTTGTATACACGCTTGCCGGAGgtatgcttgt ... gtgtatgcagTGGATTGCATTGATTGTGCAGCAGACGCATCTGTGGTGGGTGCAGTGAATG
EST: gi|88738125|gb|CI761633.1|CI761633
EST:     GATGCTGCCGATGTCAGGAATCTCTCCCTTGTATACACGCTTGCCGGAG                         TGGATTGCATTGATTGTGCAGCAGACGCATCTGTGGTGGGTGCAGTGAATG
genomic: GATGCTGCCGATGTCAGGAATCTCTCCCTTGTATACACGCTTGCCGGAGgtatgcttgt ... gtgtatgcagTGGATTGCATTGATTGTGCAGCAGACGCATCTGTGGTGGGTGCAGTGAATG
EST: gi|88763987|gb|CI773403.1|CI773403
EST:     GATGCTGCCGATGTCAGGAATCTCTCCCTTGTATACACGCTTGCCGGAG                         TGGATTGCATTGATTGTGCAGCAGACGCATCTGTGGTGGGTGCAGTGAATG
genomic: GATGCTGCCGATGTCAGGAATCTCTCCCTTGTATACACGCTTGCCGGAGgtatgcttgt ... gtgtatgcagTGGATTGCATTGATTGTGCAGCAGACGCATCTGTGGTGGGTGCAGTGAATG
EST: gi|29661372|gb|CB657647.1|CB657647
EST:     GATGCTGCCGATGTCAGGAATCTCTCCCTTGTATACACGCTTGCCGGAG                         TGGATTGCATTGATTGTGCAGCAGACGCATCTGTGGTGGGTGCAGTGAATG
genomic: GATGCTGCCGATGTCAGGAATCTCTCCCTTGTATACACGCTTGCCGGAGgtatgcttgt ... gtgtatgcagTGGATTGCATTGATTGTGCAGCAGACGCATCTGTGGTGGGTGCAGTGAATG
EST: gi|86595984|gb|CI290258.1|CI290258
EST:     GATGCTGCCGATGTCAGGAATCTCTCCCTTGTATACACGCTTGCCGGAG                         TGGATTGCATTGATTGTGCAGCAGACGCATCTGTG
genomic: GATGCTGCCGATGTCAGGAATCTCTCCCTTGTATACACGCTTGCCGGAGgtatgcttgt ... gtgtatgcagTGGATTGCATTGATTGTGCAGCAGACGCATCTGTG

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: 57 (upstream exon), 19 (downstream exon)
Score: 1

GATGCTGCCGATGTCAGGAATCTCTCCCTTGTATACACGCTTGCCGGAGgtatgcttgt ... gtgtatgcagTGGATTGCATTGATTGTGCAGCAGACGCATCTGTGGTGGGTGCAGTGAATGAAGGTATTGATGTAGCAGCCTCAATTGTGCCAGCAGTTCAAAGGCCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgtgctaggttaatctactcttgataatcatggactgattttgtgtatgcagTGGATTGCATTGATTGTGCAGCAGACGCATCTGTGGTGGGTGCAGTGAATGAAGGTATTGATGTAGCAGCCTCAATTGTGCCAGCAGTTCAAAGGCCATG
                                   gactgat  putative branch site (score: 1)
            ttaatcta  TA-rich tract