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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgccaagtcgtcgtagatttattatactatgtgtagtatttccttaaccatgcaatgcttctaagttctaaccgtgtatcattttttaaatattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA

Basic information

species Oryza sativa
transcript LOC_Os03g49420.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G033619_T02 (Zea mays), 3'ss of exon 16
ctgccaagtcgtcgtagatttattatactatgtgtagtatttccttaacc-atgcaatgcttctaagttcta--accgtgtatcattttttaaatattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA--------
  | ||| || |  |  | |  | ||| | |   |  ||| || ||||   |||  ||| | | ||||| |   ||| | ||||| ||     || | |||||||  ||||||| |||||||||||  | || ||||||||||| ||||| ||||||||| | || |||||||| || |||  |||||||||| |        
tcggcaattcat-attaactgctaatagtcttgttgctatatcattaatttatgagatg-tacaaagttttgtgaccatatatcacttggctcat-tgaacagGTAATTCCTGCCTGGTTAAGTTGCCTTCCGATAAAAAATGATTTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCAGTAAGTAA

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 16
ctgccaagtcgtcgtagatttattatactatgtgtagtatttccttaacc-atgcaatgcttctaagttcta--accgtgtatcattttttaaatattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA
  | ||| || |  |  | |  | ||| | |   |  ||| || ||||   |||  ||| | | ||||| |   ||| | ||||| ||     || | |||||||  ||||||| |||||||||||  | || ||||||||||| ||||| ||||||||| | || |||||||| || |||  |||||||||| |
tcggcaattcat-attaactgctaatagtcttgttgctatatcattaatttatgagatg-tacaaagttttgtgaccatatatcacttggctcat-tgaacagGTAATTCCTGCCTGGTTAAGTTGCCTTCCGATAAAAAATGATTTAATTGAGGCCAAGCTTGTCCATGAACAGCTGTGTGTGATGCTTGAGCA

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 17
ctgccaagtcgtcgtagatttattat--actatgtgtagtatttccttaaccatgcaatgcttctaagttctaacc-gtgtatcattttttaaatattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA
     | |  | | |  ||   | ||   |||    |  | ||| ||     ||  ||   |  |    | |   | || |   ||| | |     || ||||||||||||||| ||||| ||||| |||||||||||   ||| || |||||||||||  | |||||||| ||||| ||| | ||| |||| | 
---agaggaagccatgtatacgtcattagctagtcttgttcttttctaccatatttaactttgttggcctttcctctgtcttaaattgtgtggtatttgacagGTTGTTCCTGCCTGGTTGAGTTGCTTGCCAATAAAGGGTGATTTGATCGAGGCCAAAGTTGTTCATGACCAACTTTGTTCAATGGTTGAAAT

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|29629841|gb|CB634850.1|CB634850
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
EST: gi|27576974|gb|CA999668.1|CA999668
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
EST: gi|29629241|gb|CB634252.1|CB634252
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
EST: gi|29679232|gb|CB675507.1|CB675507
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
EST: gi|29681491|gb|CB677766.1|CB677766
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG

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: 66 (upstream exon), 69 (downstream exon)
Score: 6

CAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaccatgcaatgcttctaagttctaaccgtgtatcattttttaaatattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA
                     ttctaac  putative branch site (score: 6)
                              tgtatcattttttaaa  TA-rich tract