Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtccagttctattaaatctgtttatcctgatgaagcttttgctcattctgaattcatgatggtctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGGATTGGCTCTGTTTGTCGGATGGCTG

Basic information

species Oryza sativa
transcript LOC_Os01g60120.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60120.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G021589_T05 (Zea mays), 3'ss of exon 6
gtaatgtccagttctattaaatctgtttatcctga---------tgaagcttttgctcattctgaattca-------tgatggtctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGGATTGGCTCTGTTTGTCGGATGGCTG
||||| |||  |     ||| |||| |||    ||         || ||||     ||||| | | || |         ||| ||  || |||||||||||| ||||||||| |||||||    || |||||||||||||||||  ||||||| ||||| |||||||||
gtaatatcctttgtcgctaa-tctgcttagtaagaagtaagagctggagctacgattcattttaattttaaagtttgcaatgatcc-ctacagGTATTTGGACGTTGCTGGTCAGAAGACTTGCAATCTTTACTTATACAATGGTGTGGCTCTATTTGTTGGATGGCTG

upper sequence: LOC_Os01g60120.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G021589_T02 (Zea mays), 3'ss of exon 6
gtaatgtccagttctattaaatctgtttatcctga---------tgaagcttttgctcattctgaattca-------tgatggtctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGGATTGGCTCTGTTTGTCGGATGGCTG------------------------
||||| |||  |     ||| |||| |||    ||         || ||||     ||||| | | || |         ||| ||  || |||||||||||| ||||||||| |||||||    || |||||||||||||||||  ||||||| ||||| |||||||||                        
gtaatatcctttgtcgctaa-tctgcttagtaagaagtaagagctggagctacgattcattttaattttaaagtttgcaatgatcc-ctacagGTATTTGGACGTTGCTGGTCAGAAGACTTGCAATCTTTACTTATACAATGGTGTGGCTCTATTTGTTGGATGGCTGGTACAACAACTGCTCTCACGAGTC
















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|29664737|gb|CB661012.1|CB661012
EST:     CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATG                         GTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
genomic: CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
EST: gi|86261222|gb|CI004787.1|CI004787
EST:     ACCACTCCCTTTGTGAACCTTAGATG                         GTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
genomic: ACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
EST: gi|8859152|gb|AU096470.1|AU096470
EST:     TCATGGTTCTCTTTTACTGAAGCCACCA-TCCCTTTGTGAACCTTAGATG                         GTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
genomic: TCATGGTTCTC-TTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
EST: gi|29669063|gb|CB665338.1|CB665338
EST:     CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATG                         GTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
genomic: CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
EST: gi|29669062|gb|CB665337.1|CB665337
EST:     CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATG                         GTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
genomic: CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
EST: gi|29664738|gb|CB661013.1|CB661013
EST:     CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATG                         GTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
genomic: CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
EST: gi|8527754|gb|AU092569.1|AU092569
EST:     CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATG                         GTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
genomic: CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
EST: gi|29669064|gb|CB665339.1|CB665339
EST:     CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATG                         GTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
genomic: CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG

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: 75 (upstream exon), 44 (downstream exon)
Score: 14

TGTATGCAATCTGTCTTGCTCTGTTGAGTGGCAAAGCACACATGTACATACTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGGATTGGCTCTGTTTGTCGGATGGCTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttatcctgatgaagcttttgctcattctgaattcatgatggtctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGGATTGGCTCTGTTTGTCGGATGGCTG
       tcctgat  putative branch site (score: 14)
                                 aattcat  TA-rich tract