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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttattatatttatcaacttcttggtgatattatgcataagtagctaacatactttgcgtataatacaatctctgtaactgatcaatcagggcgaattatttcatattgtgcatacctatttctgatctggatgctattttggttttccttaactatatttctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAG

Basic information

species Oryza sativa
transcript LOC_Os07g48200.2
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 4
--------------gtatcctta---ttatatttatcaacttcttggtgatattatgcataagtagctaacatactttgcgtataatacaatctctgtaactgatcaatcagggcgaattatt-tcatattgtgcatacctattt-------ctgatctggatgctattttggttttccttaactatatttctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAG
              || ||| ||   ||  |  | | |||||| |||||| |||   |  |   |  ||   ||  ||    || |   |  ||||  ||  | ||| |  |    ||   || | ||||  ||||||  | | |       | ||| | | |  | ||||  | |||||| |||||||||   | |||||||||||||||| || || ||  |||| |||||||| || || || |||||||||||||||||||||||||||||||| |||||||| ||||| |||
gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttag--taacttatacatca---aggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttctttta-tcttccttgactatattt---tgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G172621_T01 (Zea mays), 3'ss of exon 4
--------------gtatcctta---ttatatttatcaacttcttggtgatattatgcataagtagctaacatactttgcgtataatacaatctctgtaactgatcaatcagggcgaat-tatttcatattgtgcatac-ctatttctgatctggatgctattttggtttt-----ccttaactatatttctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAG
              |  | | |    ||  | || |||||||| |||||| |||   | |    |  ||  |   | |   || ||  |    ||   ||  | ||| |  |    |   | | | ||||  ||||||   | ||| ||     |||||   ||| |||||     |||| |||||||||   |  ||||||||||||||| ||||| ||  ||||||||||||| || || || |||||||||||||||||||||||||||||||| |||||||| ||||| |||
gtatccttgataaggctttcatgcatttgaaattgtcaacttcctggtgacattgatctttgacatttagtaccttataaatacaaggc----tccagaagagctcattaggcttaagcctgtataatatgctgcataaattctttttgtaacagatgcaggttttgttttatcttccttgactatattt---tggaagTTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCTGAG

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G05840.1 (Glycine max), 3'ss of exon 6
gtatccttattatatttatcaacttcttggtgatattatgcataagtagctaacatactttgcgtataatacaatctctgtaactgatcaatcagggcgaattatttcatattgtgcatacctatttctgatctggatgctattttggttttccttaactatatttctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAG
                                                               ||||  |  |   | | ||  || |      |  |  ||      ||| |   |     || |    |  ||| |  |    | |||| |||||| | |||         ||||  || |||||  | || ||  | |||||||||||  | || |||||||||||||| || || || || |||||||| |||||||||||||| |||
---------------------------------------------------------------gtatcctttatattttttatttggttgtcttgaacatat------ataatagactctgatagtataaagttggtttattcagtagtttcccttaa-tgtatgat------agTTTGAAATCCACTGTAGTGCCATTATTTGAGAAGGTGTTGAGTGCCAGTGATGCAGGTCGAATTGGCCGTCTTGTTCTCCCAAAAGCCTGTGCTGAG

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|58671720|gb|CK060406.1|CK060406
EST:     CGATATTGGCCTAGAATAACAGACCAAGAGCTACAGCAAATTTCTGGAGA                         TTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGA
genomic: CGATATTGGCCTAGAATAACAGACCAAGAGCTACAGCAAATTTCTGGAGAgtatccttat ... tctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGA




















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), 60 (downstream exon)
Score: 25

GTGTTGCAAGGCCACCTGCAGAAGGTAGGGGCCGCAATCAATTACTTCCTCGATATTGGCCTAGAATAACAGACCAAGAGCTACAGCAAATTTCTGGAGAgtatccttat ... tctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctatttctgatctggatgctattttggttttccttaactatatttctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAG
 ttccttaac  putative branch site 
                                      ctatatttctcttc  putative PPT
                                  ttaactatatttct  TA-rich tract