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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcttcctggcttgcacaagtttattcaagtagtttttgatgcctgcatcttcaataacagttgcgatgcagGAATTTGGCAGGAAATAACTTTTCCGGTAACCTTCCATACTCGATATCCAACATGGTTTCACTCAACTATCT

Basic information

species Oryza sativa
transcript LOC_Os06g42800.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g42800.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G880265_T02 (Zea mays), 3'ss of exon 12
gtaatgcttcctggcttgcacaagtttattcaagtagtttttgatgcctgcatcttcaataacagttgcgatgcagGAATTTGGCAGGAAATAACTTTTCCGGTAACCTTCCATACTCGATATCCAACATGGTTTCACTCAACTATCT
||||||  |||   | || |||  || ||| |  |  | || |||   || |  || | | | ||     || ||||||| |||||  ||||||||| || ||||| ||||||||||| ||||||||| ||||||||||  | || ||
gtaatgtctcccaacctgtacatatt-attga--tgctattcgatttttgaaatttgattcaaagcg--aatacagGAATCTGGCAAAAAATAACTTCTCTGGTAATCTTCCATACTCTATATCCAACTTGGTTTCACTTGAGTACCT

upper sequence: LOC_Os06g42800.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G162531_T02 (Zea mays), 3'ss of exon 3
--------------------------------------gtaatgcttcctggcttgcacaagtttattcaagtagtttttgatgcctgcatcttcaataacagttgcgatgcagGAATTTGGCAGGAAATAACTTTTCCGGTAACCTTCCATACTCGATATCCAACATGGTTTCACTCAACTATCT
                                      ||||||  |||   | || |||  || |||||  |  | || ||| | || |  || | | | ||     || ||||||| |||||  ||||||||| |||||||| ||||||||||| ||||||||| ||||||||||  | || ||
tcaatcccttaccagttgccatcaaaccttacctatctgtaatgtctcccaacctgtacatatt-attca--tgctattcgattcttgaaatttgattcaaagCG--AATACAGGAATCTGGCAAAAAATAACTTCTCCGGTAATCTTCCATACTCTATATCCAACTTGGTTTCACTTGAGTACCT

upper sequence: LOC_Os06g42800.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G162531_T04 (Zea mays), 3'ss of exon 1
gtaatgcttcctggcttgcacaagtttattcaagtagtttttgatgcctgcatcttcaataacagttgcgatgcagGAATTTGGCAGGAAATAACTTTTCCGGTAACCTTCCATACTCGATATCCAACATGGTTTCACTCAACTATCT
||||||  |||   | || |||  || |||||  |  | || ||| | || |  || | | | ||     || ||||||| |||||  ||||||||| |||||||| ||||||||||| ||||||||| ||||||||||  | || ||
gtaatgtctcccaacctgtacatatt-attca--tgctattcgattcttgaaatttgattcaaagcg--aatacagGAATCTGGCAAAAAATAACTTCTCCGGTAATCTTCCATACTCTATATCCAACTTGGTTTCACTTGAGTACCT

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: 50 (upstream exon), 52 (downstream exon)
Score: 6

GGACTTGAGTAGCAACAACTTGCATGATTCAATTCCTTATCAGCTGCCACCAAATCTCGCCTATCTgtaatgcttc ... tgcgatgcagGAATTTGGCAGGAAATAACTTTTCCGGTAACCTTCCATACTCGATATCCAACATGGTTTCACTCAACTATCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtttattcaagtagtttttgatgcctgcatcttcaataacagttgcgatgcagGAATTTGGCAGGAAATAACTTTTCCGGTAACCTTCCATACTCGATATCCAACATGGTTTCACTCAACTATCT
                                   caataac  putative branch site (score: 6)
             tagttttt  TA-rich tract