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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACATCAGTGGAAGCGCACATTTCATAAACAAATGTGATAATGGAATTGTCATCCATCGAAACAGGGATCCAAACAGTGGCCCACTTGATGTTGTGCAGgttacttttgccctctttattaccttataagttaaaatcttaatgcttcaatttagggcctcgcctaactcgtgtatttttttatattatgttggggttggattgggttatcacag

Basic information

species Oryza sativa
transcript LOC_Os06g45980.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G164835_T01 (Zea mays), 5'ss of exon 19
TGACATCAGTGGAAGCGCACATTTCATAAACAAATGTGATAATGGAATTGTCATCCATCGAAACAGGGATCCAAACAGTGGCCCACTTGATGTTGTGCAGgttacttttgccctctttattaccttataagttaaaatcttaatgcttcaatttagggcctcgcctaactcgtgtatttttttatattatgttggggttggattgg-gttatcacag
 ||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||  |||||||||| |||||   |||||| ||||||   |||||||||| |||||| ||| || ||||| | |     |  |  ||  |   || ||||  |         || |    | | | |  |     |  |     |   | |  ||||||||||
CGACATAAGTGGAAGCGCACATTTTATAAACAAATGTGATAATGGAATTGTCATCCACAGAAACAGGGACCCAAATGCTGGCCCCCTTGATACCGTGCAGgttatttttgctctcatttttaccctttcttcaatgagatttgtttatccatttttgttacgaagaaatttaattgtgtgtcaacccctttgttctactacctggctgttatcacag

upper sequence: LOC_Os06g45980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: AT1G30680.1 (Arabidopsis thaliana), 5'ss of exon 17
TGACATCAGTGGAAGCGCACATTTCATAAACAAATGTGATAATGGAATTGTCATCCATCGAAACAGGGATCCAAACAGTGGCCCACTTGATGTTGTGCAGgttacttttgccctctttattaccttataagttaaaatcttaatgcttcaatttagggcctcgcctaactcgtgtatttttttatattatgttggggttggattgggttatcacag
 || || ||||| ||||||||||| |||||||||||||| ||||| ||| |  | ||  ||||| | ||   |||   ||| || |||||| | || || ||   |      | ||| ||   | | |    |||  | |||    ||  |   | |||||  | ||    ||  | ||  | |  || |  |  | ||                 
CGATATTAGTGGCAGCGCACATTTTATAAACAAATGTGACAATGGTATTATAGTTCACAGAAACCGCGACGAAAATGCTGGACCTCTTGATCTAGTTCAAgtgggtaccaatcccttcatcttcatctg---taatgtatta----ttttaaaaatggcctt-cttattgtgtaaagttactaacctttttgtatgttttag--------------

upper sequence: LOC_Os06g45980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv18s0001g01350.t01 (Vitis vinifera), 5'ss of exon 6
TGACATCAGTGGAAGCGCACATTTCATAAACAAATGTGATAATGGAATTGTCATCCATCGAAACAGGGATCCAAACAGTGGCCCACTTGATGTTGTGCAGgttacttttgccctc----------tttattaccttataagttaaaatcttaatgcttcaatttagggcctcgcctaactcgtgtatttttttatattatgtt---ggggttggattgggttatcacag------------------------
||| ||||||||||| ||||| |||||||| |||||||| ||||||||||| || ||||| ||  |  ||||| |   ||| ||  |||||   ||||| ||   |||     ||          ||||| |  |||| |||    ||||   |  ||    || |      |   ||   |||  |     |  || | | |   ||  | | |     || | | |                         
TGATATCAGTGGAAGTGCACACTTCATAAATAAATGTGACAATGGAATTGTTATTCATCGTAATCGAAATCCAGATGCTGGGCCTGTTGATCAAGTGCAAgtaggtttcattttcgaagttttattttatcaatttattagtggttatctatttatttgttcttggaaaaaggaagaaaaggtggttggccattcatcaaggttcaggaatggaaacttattcttaaaaaactcttaaattatcaatttgcag

upper sequence: LOC_Os06g45980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv10s0003g05490.t01 (Vitis vinifera), 5'ss of exon 19
TGACATCAGTGGAAGCGCACATTTCATAAACAAATGTGATAATGGAATTGTCATCCATCGAAACAGGGATCCAAACAGTGGCCCACTTGATGTTGTGCAGgttacttttgccctc---------tttattaccttataagttaaaatcttaatgcttcaatttagggcctcgcctaactcgtgtat---ttttttatattatgttggggttggattgggttatcacag-----------------------
||| ||||||||||| ||||| |||||||| |||||||| ||||||||||| || ||||| ||  |  ||||| |   ||| ||  |||||   ||||| ||   |||      |         ||||| |  || | | |    ||||   |  ||    || |      | | ||   |||  |     ||||  |   |   ||  | | |     || | | |                        
TGATATCAGTGGAAGTGCACACTTCATAAATAAATGTGACAATGGAATTGTTATTCATCGTAATCGAAATCCAGAAGCTGGGCCTGTTGATCAAGTGCAAgtaggtttcatttacgaagtttattttatcaatttgttattggttatctatttatttgttcttggaaaaaggacaaaaaggtggttggccatttttcaaggttcaggaatggaaacttattcttaaaatctcttaaattatcaatttgcag

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|8859296|gb|AU096614.1|AU096614
EST:     TCATCCATCGAAACAGGGANCCAAACAGTGGCCCACTTGATGTTGTGCAG                         GTTTGTGTGAGGAAGGTGCGCAACAAAGTGATTGGACAAATAGGAGATGCT
genomic: TCATCCATCGAAACAGGGATCCAAACAGTGGCCCACTTGATGTTGTGCAGgttacttttg ... gttatcacagGTTTGTGTGAGGAAGGTGCGCAACAAAGTGATTGGACAAATAGGAGATGCT
EST: gi|25803007|gb|CA758968.1|CA758968
EST:     ATCCATCGAAACAGGGATCCAAACAGTGGCCCACTTGATGTTGTGCAG                         GTTTGTGTGAGGAAGGTGCGCAACAAAGTGATTGGACAAATAGGAGATGCT
genomic: ATCCATCGAAACAGGGATCCAAACAGTGGCCCACTTGATGTTGTGCAGgttacttttg ... gttatcacagGTTTGTGTGAGGAAGGTGCGCAACAAAGTGATTGGACAAATAGGAGATGCT
EST: gi|396941545|gb|HO188754.1|HO188754
EST:     TCATCCATCGAAACAGGGATCCAAACAGTGGCCCACTTGATGTTGTGCAG                         GTTTGTGTGAGGAAGGTGCGCAACAAAGTGATTGGACAAATAGGAGATGCT
genomic: TCATCCATCGAAACAGGGATCCAAACAGTGGCCCACTTGATGTTGTGCAGgttacttttg ... gttatcacagGTTTGTGTGAGGAAGGTGCGCAACAAAGTGATTGGACAAATAGGAGATGCT

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: 65 (upstream exon), 68 (downstream exon)
Score: 10

TGACATCAGTGGAAGCGCACATTTCATAAACAAATGTGATAATGGAATTGTCATCCATCGAAACAGGGATCCAAACAGTGGCCCACTTGATGTTGTGCAGgttacttttg ... gttatcacagGTTTGTGTGAGGAAGGTGCGCAACAAAGTGATTGGACAAATAGGAGATGCTTTCTTGTCATATGAACG




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