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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG

Basic information

species Oryza sativa
transcript LOC_Os04g41470.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 9
---------gtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggtt----aatttgtgc-tgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
          |    ||| ||||||| || |||| |     ||  |  ||||   |    || |    ||    ||||| |   || || |   ||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||
gtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaatttgggtcatgtactagattttctgaatttatttatgttttgttgtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
---------gtacagttctaatctgagatattttcttaatactttattattt---ttatttaata-----ttgtggttaatttgtgct--gcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
          | |  ||| ||||| | || |||| |     ||  |   |||   | || || ||     |     || |||| || |  | || |   ||  |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||| ||||||||||||||||||
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 9
gtac-agttcta-atctgagatattttcttaa-tact--ttattatttttatttaatattgtggttaatttgtgctgcttcgcactggtt----acagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
|||  ||||||  |  |    ||| ||| | | ||     || ||| | ||||||   |||    || ||| ||    |||  | |  ||     |||||||||||  ||||||   |  |||| |||||||||||||| |||||||||||||| ||||| |||||  | |||||| ||||||| |||
gtatgagttctgtacattgtttatgttcctgactaacaactaatatgtctatttatctttgaacatattttttgtc-tttcataatctttctgtgcagTATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCG

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------gtacagttctaatctgagatattt-tcttaatactttattatttttatt-taatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
                  |  || |   || |||| ||||     | | || |  |  ||  |||   | |  | |  | | ||   |   | |  || |||||||||||| | ||  ||||||| |||||||| ||||||||||||||  | |||||||| || |||||||| |||||  | ||  | || 
tagaggctggcacttgaattcaagcgacgagatttatcttttgggtctgttttcctagttacaatccagagagtgacgtttacttagtttgagt--ttgcagTATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCT

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 3'ss of exon 10
gtacagttctaatctgagatattttcttaatactttattatt-------tttatttaatattgtggttaatttgtgctgcttcgcactggtta------cagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
     ||  || | ||  | |  | ||    |  || |   |       ||  || ||  |  |  | |||||| |||   |   || | | |      |||||||||||| | ||  ||||||| |||||||| |||||||| |||||  | || |||||||||||||| || |||||  | ||  | || 
agctggtcatactttgcaacaggtcctagccatattctaggtgacagaattctttcaaagtcct--tgaatttgagctaactgctacagttcattcttccagTATGATGAAGCAGAGCGGAGAAGGGAAATGGCGAAGAACTCCCTTGAACGTTACACACACTATTATGAGCGTTGGGCTACAAACGAATCT

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ08409 (Selaginella moellendorffii), 3'ss of exon 9
gtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
                           ||  | || || ||||   |||    |   ||   | |  | ||| ||       || |||||| |||||| |||| ||||| || |||||||| ||||||||| | |||||||||||||| || || || || |||||  | ||  | || 
--------------------------gtaccaattgat-atttacgtttcccttcacgg---actcatcctgtttgt-----gtaacagTACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ15174 (Selaginella moellendorffii), 3'ss of exon 9
gtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
                           ||  | || || ||||   |||    |   ||   | |  | ||| ||       || |||||| |||||| |||| ||||| ||||||||||| ||||||||| | |||||||||||||| || || || || |||||  | ||  | || 
--------------------------gtaccaattgat-atttacgtttcccttcacgg---actcatcctgtttgt-----gtaacagTACGATGAAGCTGAGAGGAGGAGAGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ16231 (Selaginella moellendorffii), 3'ss of exon 9
gtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG----------
                              ||| |   ||    || ||   | ||     |||||       |||       ||||||||||||||| |||||||| | ||||| ||||| ||||||  ||||||  | ||||||||||| || ||| | |||||  | ||  ||||           
-----------------------------gtacgtatctagg--tagttctcactgcctcaaatttacaagttttc-------ttacagTATGATGAAGCTGAAAGGCGTAGAGAGATGGCTAAGAACATGCTTGAACGTTATACACACTACTACGAAAGATGGGCCACAAACGAGTCATCCAGGCAAA

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ17699 (Selaginella moellendorffii), 3'ss of exon 9
gtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG----------
                              ||| |   ||    || ||   | ||     | |||       |||       ||||||||||||||| |||||||| | ||||| ||||| ||||||  ||||||  | ||||||||||| || ||| | |||||  | ||  ||||           
-----------------------------gtacgtatctagg--tacttctcactgcctcaactttacaaattttc-------ttacagTATGATGAAGCTGAAAGGCGTAGAGAGATGGCTAAGAACATGCTTGAACGTTATACACACTACTACGAAAGATGGGCCACAAACGAGTCATCCAGGCAAA

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|29614534|gb|CB619547.1|CB619547
EST:     GTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG                         TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGA
genomic: GTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCGgtacagttct ... ctggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGA
EST: gi|66920746|gb|CX107594.1|CX107594
EST:     GTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG                         TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGA
genomic: GTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCGgtacagttct ... ctggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGA

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), 75 (downstream exon)
Score: 62

GCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCGgtacagttct ... ctggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
                       ggttaat  putative branch site (score: 62)
     atttttatttaatatt  TA-rich tract