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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggagatattgaaaatattttcctttaggctatgtttgtttggcttcattttcttttagtttgtttttcgtcattgcgttttcttctttttatcttcactaaacatttcttttgtggccag

Basic information

species Oryza sativa
transcript LOC_Os05g42350.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g42350.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G090338_T01 (Zea mays), 5'ss of exon 6
TGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggagatattgaaaatattttcctttaggctatgtttgtttggcttcattttcttttagtttgtttttcgtcattgcgttttcttctttttatcttcactaaacatttcttt--tgtggccag--
 ||||| || || ||||||||||| || |||||||||||||||||||||||||||||||||||| |||| |||||||||||||||||||| ||||||||||||      ||| ||  | ||||||       |  |  |   ||||  | ||||  |||     |  |   |  | | |   |||| ||  |||| | || | |  ||  | || |  ||||||||   
GGAGTCTGTGGTTGTGAGGATAACTGGATGCCCTAATGGATGCGCTAGACCATATATGGCAGAGCTTGGTTTTGTTGGTGATGGCCCAAAAAGTTACCAGgtaacaagaatagtggca-tatttt-------gacacatcattttgattacattcacttggcaatcttacctatttagttttttttgtttattttgtatttattgcactctactctactgtggccatag

upper sequence: LOC_Os05g42350.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA12G02200.1 (Glycine max), 5'ss of exon 6
TGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggagatattgaaaatattttcctttaggctatgtttgtttggcttcattttctttta-gtttgtttttcgtcattgcgttttcttctttttatcttcactaaacatttcttttgtggccag
|||||| || || || |||||||| |||||||||||||| || ||||||||||| ||||| ||| ||||  | ||||||||||||||||| || || ||||| | |  |||  || |  |    ||  | |   |  | | |    |||  |    || | | |||   | ||  |  ||  | |                                         
TGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAGCTTGGACTAGTTGGTGATGGCCCAAATAGCTATCAGgt-ttgttgat-ctgcagctgaactcgctgacagtg-gatagaaaagctcaaaagactataatgttcactgttttttcttatgatgcag-------------------------------------

upper sequence: LOC_Os05g42350.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA11G09890.1 (Glycine max), 5'ss of exon 6
TGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggagatattgaaaatattttcctttaggctatgtttgtttggcttcattttcttttagtttgtttttcgtcattgcgttttcttctttttatcttcactaaacatttcttttgtggccag
|||||| || || || |||||||| |||||||||||||| || ||||||||||| ||||| ||  ||||  | ||||||||||| ||||| || || ||||| |       ||    |       ||  |      || | |    |||  ||        || ||    |   ||| ||  |||| ||||| | ||                            
TGAGTCTGTGGTTGTAAGGATAACTGGCTGCCCTAATGGTTGTGCTAGACCATACATGGCTGAACTTGGACTAGTTGGTGATGGTCCAAATAGCTATCAGgtttgttg---atcagcagctgaacccgctgacagttgatagaaaagctcaat--------agattaccatgt-tcactgt-tttttttcttctgatgcag------------------------

upper sequence: LOC_Os05g42350.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S47_171V6.2 (Physcomitrella patens), 5'ss of exon 4
TGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtatagga---gatattgaaaa----tatt-ttcctttag--gctatgtttgtttg-----gcttcattttctttt-agtttgtttttcgtcattgcgttttcttctttttatcttcactaaacatttcttttgtggccag
 |||||  | |||||  | || || |||||||||||||| || || || || || ||||||||| |||| || ||||| ||||| || ||||| |||||||||||       |  |||| ||    |||| || | |||   ||||| ||||  ||     |||       ||||| |||  |  ||   |  ||  ||    |||| |||    ||  ||                    
AGAGTCCCTGGTGGTTCGCATTACTGGCTGCCCTAATGGTTGTGCAAGGCCGTACATGGCAGAGCTTGGATTAGTTGGCGATGGACCCAACAGCTACCAGgtataatttccaactttgacaaaaattattgttgccttaacagctatatttgcatgataatgctatggccacttttgagtacgacttgaatggtttggtgcatttctgttttctctctgtag-------------------

upper sequence: LOC_Os05g42350.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S160_137V6.1 (Physcomitrella patens), 5'ss of exon 5
TGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggagatattgaaaatattttcctttaggctatgtttgtttggcttcattttcttttagtttgtttttcgtcattgcgttttcttctttttatcttcactaaacatttcttttgtggccag
 || ||| | |||||||| || || ||||||||||| || || ||||| ||||| ||||||||| | ||  | |||||||| ||||||||||| |||||||||||    | ||      |   |||       || |  ||    | |     |   ||||||||  |||||   | ||| |     |    |||   |    | |    || |  ||  |    
GGAATCGCTGGTGGTGAGAATTACCGGCTGCCCTAACGGGTGTGCTAGGCCATACATGGCAGAGCTCGGACTAGTTGGTGACGGCCCAAACAGCTACCAGgtataattta-atgtcttgtcgcttcgcaagcactctagttcacagaccaacatcagttttagttaatttttttcctttgtgaaacttagggtttcaatctgttga----ttgtggtgcag----

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|10794927|gb|AU108893.1|AU108893
EST:     CATNTATGGCAGAGGTTGGCTTTNTTGGTGATGGCCCAAACAGTTACCAG                         ATATGGCTTGGAGGAACNCCAAACCAGAGTACCCTAGCTGAAACCTTTATG
genomic: CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggaga ... ttgtggccagATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
EST: gi|58691385|gb|CK080072.1|CK080072
EST:     CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCATACAGTTACCAG                         ATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
genomic: CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggaga ... ttgtggccagATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
EST: gi|29621655|gb|CB626666.1|CB626666
EST:     CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAG                         ATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
genomic: CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggaga ... ttgtggccagATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
EST: gi|58694341|gb|CK083028.1|CK083028
EST:     CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAG                         ATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
genomic: CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggaga ... ttgtggccagATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
EST: gi|5002798|gb|AU067907.1|AU067907
EST:     CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAG                         ATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
genomic: CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggaga ... ttgtggccagATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
EST: gi|2311250|gb|C27405.1|C27405
EST:     CATATATGGCAGAGGTTGGCTTTNTTGGTGATGGCCCAAACAGTTACCAG                         ATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
genomic: CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggaga ... ttgtggccagATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
EST: gi|88216162|gb|CI216011.1|CI216011
EST:     AGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAG                         ATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
genomic: AGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggaga ... ttgtggccagATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
EST: gi|86495058|gb|CI137691.1|CI137691
EST:     CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAG                         ATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
genomic: CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggaga ... ttgtggccagATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
EST: gi|89176027|gb|CI043048.1|CI043048
EST:     CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAG                         ATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
genomic: CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggaga ... ttgtggccagATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
EST: gi|29625861|gb|CB630872.1|CB630872
EST:     CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAG                         ATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG
genomic: CATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggaga ... ttgtggccagATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATG

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: 73 (upstream exon), 72 (downstream exon)
Score: 29

TGAGTCGGTAGTGGTGAGGATAACAGGCTGCCCTAATGGATGCGCTAGACCATATATGGCAGAGGTTGGCTTTGTTGGTGATGGCCCAAACAGTTACCAGgtataggaga ... ttgtggccagATATGGCTTGGAGGAACACCAAACCAGAGTACCCTAGCTGAAACCTTTATGAATAAAGTGAAGCTTCAAGATATTGAGAAGGTTTTGGAACCATTGTTTT




<











<


<