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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactatctttccagattaaaccagcgcttttcttttcttttcatattggagatgatggacatgatttgcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTCCATCATGGTGACACCAGATTCTACTCAAGTGATTGATCCAGAATTTGCT

Basic information

species Oryza sativa
transcript LOC_Os04g57400.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57400.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G464137_T03 (Zea mays), 3'ss of exon 3
gtaactatctttccagatt-aaaccagcg----cttttcttttcttttcatat-tggagatgatggacat----gatttgcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTCCATCATGGTGACACCAGATTCTACTCAAGTGATTGATCCAGAATTTGCT
|||| || ||  |   ||| |||  || |    | | | |||| |||   ||  |||  ||  ||    |    | ||| ||  ||||||||||| |||||||| || |||||  ||||||||||||||||||||||||| |||||||||||   || ||| |||||||| ||||||||||||||||  
gtaattacctcactgaattgaaattagtggccacctgtgttttgtttctgtacatgggaattgtgactttttttggtttccaactgcagGTTTATCGAGAGAGCTCAAGCTCTGATTCATGGAGATCTCCACACTGGTTCTATCATGGTGACCGAAGGTTCAACTCAAGTCATTGATCCAGAATTTGGG

upper sequence: LOC_Os04g57400.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G26580.1 (Glycine max), 3'ss of exon 3
-----gtaactatctttccagattaaaccagcgcttttcttttcttttcatattggagatgatggacatg---atttgca--tatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTCCATCATGGTGACACCAGATTCTACTCAAGTGATTGATCCAGAATTTGCT
     ||  || |||||   | ||  |||     | | || |  |||   | || ||  |  |    ||    ||||       || ||||| |||||||| || ||||| ||  | ||||||||||| |||||||||||  | ||||| || |  || || |||||||| ||||||||||||||||| 
gtattgtggctctcttt---gtttttacccattatatgctgtagtttcgttgttagattttttctttataggaatttatggtcctgtagGTTCATTGAGAGGGCCCAGGCACTAATACATGGAGATCTACACACTGGTTCTGTGATGGTTACTCGTGAATCAACTCAAGTTATTGATCCAGAATTTGCA

upper sequence: LOC_Os04g57400.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G40730.1 (Glycine max), 3'ss of exon 3
------gtaactatctttccagattaaaccagcgcttttcttttcttttcatattggagatg-atggacatgatttgcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTCCATCATGGTGACACCAGATTCTACTCAAGTGATTGATCCAGAATTTGCT
       ||   |  |||    |   |      ||  |  |||| || | | |||     |  || |  ||  | ||    || ||||| |||||||| || ||||| ||  | ||||||||||| |||||||||||  | ||||| || |  || || |||||||| ||||||||||||||||| 
gtattattactcacttttttttacccattatatgcagtagttttgttgttagattttttctttataggaatt-tatgttcctgtagGTTCATTGAGAGGGCCCAGGCACTAATACATGGAGATCTACACACTGGTTCTGTGATGGTTACCCGTGAATCAACTCAAGTTATTGATCCAGAATTTGCA

upper sequence: LOC_Os04g57400.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv03s0091g00100.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------gtaactatctttccagattaaaccagcgcttttcttttcttttcatattggaga---tgatggacatgatttgcatat-----gcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTCCATCATGGTGACACCAGATTCTACTCAAGTGATTGATCCAGAATTTGCT
                                      ||   |   || |   | | | |||     ||||    |   ||  ||| |     |  |   | |  || | || |     |||||||   ||||||| | || || ||  | ||||||||||| || ||||||||  | ||||| || || ||||| |||||||| || |||||||||||||  
gtactgtttccatatcagtgcctcatttcttgcagtaatataaaatgtttctattaatagcagtttaattctgaaataaacaggttgaaatcctttctaagcctagttagaatctattttgcagGTTCTGTGAGAGATCGCAAGCCCTAGTACATGGAGATCTTCATACTGGTTCAGTTATGGTTACCCCTGATTCGACTCAAGTTATAGATCCAGAATTTGGC

upper sequence: LOC_Os04g57400.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv03s0091g00080.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------gtaactatctttccagattaaaccagcgcttttcttttcttttcatattggag--------atgatggacatgatttgcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTCCATCATGGTGACACCAGATTCTACTCAAGTGATTGATCCAGAATTTGCT
                                      ||   |   || |   | | | |||     ||||    |   ||  ||| |         |||        || |    | ||||||||   ||||||| |||| || ||  | ||||||||||| || ||||||||  | ||||| || || ||||| |||||||| || |||||||||||||  
gtagtgcttccatatcagtacctcatttctttacgtaatataaaatatttctattaatagcagtttaattctgaagtaaacaggttgaaatcctttctatgcctagttagaatctattttgcagGTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTCAGTTATGGTTACCCCTGATTCGACTCAAGTTATAGATCCAGAATTTGGA

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|66915549|gb|CX102397.1|CX102397
EST:     GTTCGAGAGGATGCTGAGCTTAAATTGGAGATTGCTGAATTGAAATCAAT                         GTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
genomic: GTTCGAGAGGATGCTGAGCTTAAATTGGAGATTGCTGAATTGAAATCAATgtaactatct ... gcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
EST: gi|428869|gb|D25025.1|D25025
EST:     GTTCGAGAGGATGCTGAGCTTAAATTGGAGATTGCTGAATTGAAATCAAT                         GTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
genomic: GTTCGAGAGGATGCTGAGCTTAAATTGGAGATTGCTGAATTGAAATCAATgtaactatct ... gcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
EST: gi|27576663|gb|CA999357.1|CA999357
EST:     GTTCGAGAGGATGCTGAGCTTAAATTGGAGATTGCTGAATTGAAATCAAT                         GTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
genomic: GTTCGAGAGGATGCTGAGCTTAAATTGGAGATTGCTGAATTGAAATCAATgtaactatct ... gcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
EST: gi|218504013|gb|FG946243.1|FG946243
EST:     GTTCGAGAGGATGCTGAGCTTAAATTGGAGATTGCTGAATTGAAATCAAT                         GTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
genomic: GTTCGAGAGGATGCTGAGCTTAAATTGGAGATTGCTGAATTGAAATCAATgtaactatct ... gcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
EST: gi|27576846|gb|CA999540.1|CA999540
EST:     GTTCGAGAGGATGCTGAGCTTAAATTGGAGATTGCTGAATTGAAATCAAT                         GTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
genomic: GTTCGAGAGGATGCTGAGCTTAAATTGGAGATTGCTGAATTGAAATCAATgtaactatct ... gcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
EST: gi|88359320|gb|CI679847.1|CI679847
EST:     GAATTGAAATCAAT                         GTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
genomic: GAATTGAAATCAATgtaactatct ... gcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
EST: gi|88412647|gb|CI690393.1|CI690393
EST:     GAATTGAAATCAAT                         GTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
genomic: GAATTGAAATCAATgtaactatct ... gcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
EST: gi|88583470|gb|CI700952.1|CI700952
EST:     GAATTGAAATCAAT                         GTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
genomic: GAATTGAAATCAATgtaactatct ... gcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
EST: gi|29626238|gb|CB631249.1|CB631249
EST:     GTTCGAGAGGATGCTGAGCTTAAATTGGAGATTGCTGAATTGAAATCAAT                         GTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC
genomic: GTTCGAGAGGATGCTGAGCTTAAATTGGAGATTGCTGAATTGAAATCAATgtaactatct ... gcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTC

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: 62 (upstream exon), 59 (downstream exon)
Score: 48

CCAAATACAATCGTTGCACATCACCCTTCCTAGATAATGATGCTGCAGCGGTTCGAGAGGATGCTGAGCTTAAATTGGAGATTGCTGAATTGAAATCAATgtaactatct ... gcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTCCATCATGGTGACACCAGATTCTACTCAAGTGATTGATCCAGAATTTGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgcttttcttttcttttcatattggagatgatggacatgatttgcatatgcagGTTTATTGAGAGAGCACAGGCTCTTCTTCATGGAGATCTCCACACTGGTTCCATCATGGTGACACCAGATTCTACTCAAGTGATTGATCCAGAATTTGCT
          ttttcttttcatatt  TA-rich tract