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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgatggttctagtgtgtgttgttttaatgcttaacttaaatggtgctcattacttaattgctaatattccattctatctcatgcagATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGAGATATAAAGCCACAAAATATCTTG

Basic information

species Oryza sativa
transcript LOC_Os06g35530.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g35530.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G043350_T01 (Zea mays), 3'ss of exon 4
gtgggtgatggttctagtgtgtgttgttttaat--gcttaacttaaatggtgctcattacttaattgctaatattccattctatctcatgcagATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGAGATATAAAGCCACAAAATATCTTG
||||||  ||||   | ||  |  | | || ||  || |    || | |  |    | |  || || |  || || |||   ||||  ||||||||||||| ||| ||||||| ||||| ||||| || ||| |||||||||||||||| ||||| || |||||||||
gtgggtagtggtagaattgcattctatcttgatatgcatgtgctagaagaggtgtttaatatatttac--atttttcat---atcttgtgcagATATTCCGGGGACTAGCTTATATTCATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTG
















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|58678104|gb|CK066791.1|CK066791
EST:     ATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAG                         ATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGA
genomic: ATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAGgtgggtgatg ... tctcatgcagATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGA
EST: gi|15008260|gb|AU222648.1|AU222648
EST:     ATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAG                         ATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGA
genomic: ATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAGgtgggtgatg ... tctcatgcagATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGA
EST: gi|29672896|gb|CB669171.1|CB669171
EST:     ATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAG                         ATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGA
genomic: ATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAGgtgggtgatg ... tctcatgcagATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGA
EST: gi|58680026|gb|CK068713.1|CK068713
EST:     AGAGGATG-CACTTATATATGTCAAACTTTACATGTATCAG                         ATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAG-TTGTCACCGA
genomic: AGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAGgtgggtgatg ... tctcatgcagATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGA
EST: gi|58605154|gb|CK033187.1|CK033187
EST:     ATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAG                         ATATTCCGCGGATTAGCTTACATTCACACTGTTCCTAGAGTTTGTCACCGA
genomic: ATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAGgtgggtgatg ... tctcatgcagATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGA
EST: gi|88725747|gb|CI749006.1|CI749006
EST:     ATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAG                         ATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGA
genomic: ATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAGgtgggtgatg ... tctcatgcagATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGA
EST: gi|29689142|gb|CB685417.1|CB685417
EST:     ATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAG                         ATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGA
genomic: ATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAGgtgggtgatg ... tctcatgcagATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGA
EST: gi|29660849|gb|CB657124.1|CB657124
EST:     ATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAG                         ATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGA
genomic: ATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAGgtgggtgatg ... tctcatgcagATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGA

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: 69 (upstream exon), 65 (downstream exon)
Score: 49

CATGGAGTTTGTTCCCGAGTCACTTTATCGTGTCCTGAAACACTACAAAGATATGAAGCAGAGGATGCCACTTATATATGTCAAACTTTACATGTATCAGgtgggtgatg ... tctcatgcagATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGAGATATAAAGCCACAAAATATCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacttaaatggtgctcattacttaattgctaatattccattctatctcatgcagATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGAGATATAAAGCCACAAAATATCTTG
                           tgctaat  putative branch site (score: 49)
                                   ttccattctatctc  CT-rich tract
                      ttaattgctaatatt  TA-rich tract