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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttttgagagcttggattttatcctatgtttatactttatataatgatggaaccactatttagttgattatcaattcttcgttttctttttctagGTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGT

Basic information

species Oryza sativa
transcript LOC_Os05g28180.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28180.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G416667_T03 (Zea mays), 3'ss of exon 9
----gtgtgttttgagagcttggattttatcctatgtttatactttatataatgatggaaccactatttagttgattatcaattcttcgttttctttttct-agGTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGT
    ||   || |      | |||| |  |   |     ||   ||   || |  |   ||   | || |    | | |    |  |  || |  |||||| ||||||||  ||||||||||||| |||||||||||||| |||||||| |||||||||||||||||||||||||| || || |||||||| ||||||||||||
acatgtacattctcccctttcggatatagtaacaa----atgagttgcctattcctaatacatatgttgacactactgttggcttataattcttattttctcagGTATGATCTGAATGTTGATTTGCTAGATGTCCATGCAGACAAAAGCACATTTCATCGTTTTGACAAATTCAATCTAAAATACAATCCATGTGGCCAAAGT

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------------------------------------------------------gtgtgttttgagagct-tggatt--ttatcctatgtttatactttatataatgatggaaccactatttagttgattatcaattcttcgtttt--ctttttctagGTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGT
                                                                                             |   | ||| |  |    ||||   | |  |   ||| |      | | |  |||  |||   |   | || |   |     ||| ||||   | ||    || |||||| |||| || ||  |  | ||||| ||||| ||||||||||| |||||||||||||| || |||||||| ||||| || || ||||| ||||||
gtaattacatttccaacttcttagaattcccaacttaactctatctgaatctgatggctgcaagactattagattaccctcttaggagcctcctagttgttgcgcaccgcagattgcctgtattgcattttttaccatttttaccatgacaccg--aagaaattaacctttttccctttgtttgaacattgcacagATATGACCTGAACGTCGACCTTTTGGATGTTCATGCAGACAAAAGTACCTTTCATCGTTTTGATAAGTTCAACCTAAAGTATAACCCTTGTGGTCAAAGT

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 8
------------------------------------------gtgtgttttgagagcttggattttatcctatgtttatactttatataatgatggaaccactatttagttgattatcaattcttcgttttctttttctagGTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGT
                                           ||||| |   | |  || | ||| |   |  |||      | ||  ||  || |||      | | |  |   ||| |      |||| |||    ||||||||| ||||||||||  |  ||||||| ||||| ||||| || ||||||||||||||||| || ||||| || ||||||||||| || || ||||||
gtaataaaaatttgtttttttttttaatactatttgaccaagatgtgtgtgtggggagtgtaattttttacaccttttagtcatttaccattttgaaact----ctgaatataacctcactgaac--ttttgtttgaacagGTATGACCTGAATGTTGACCTTTTAGATGTTCATGCAGACAAGAGCACATTTCATCGTTTTGATAAGTTCAATCTCAAGTACAATCCCTGCGGTCAAAGT

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 3'ss of exon 8
gtgtgttttgagagcttggat-tttatcctatgtttatactttatataatgatggaaccactatttagttgattatcaattct----tcgttttctttttctagGTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGT
    | |||       |   | ||| |  |   ||| ||   ||||  |   || ||  | | |   ||  ||   |  | ||    | || |     ||  || || ||| | ||||| || || || ||||| ||||| ||||||| ||| ||||||||||| ||||| |||||||| || |||||||| |||||||| |||
----gctttcgtcttctaattatttttgtttcctttttatagtataccactttgaaatgattttcatgtatatctaccgtgctggtcttgtgtctgaattgcagTTACGACCTTAATGTGGACTTGCTGGATGTTCATGCTGACAAAAATACGTTTCATCGTTTCGACAAGTTCAACCTGAAATACAATCCTTGTGGCCAGAGT

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 8
---gtgtgttttgagagcttggattttatcctatgtttatacttta-tataatgatggaaccactatttagttgattatcaattcttcgttttctttttctagGTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGT
    | |||         ||  |   || |  || ||||||| ||| |    | | |     | |   | ||    |||   |  || || | | |||   || |||||  | ||||| ||||| || ||||||||||| ||||| | ||||||||| || || ||||| |||||| | ||||| ||||| |||||||| |||
tcaatttgtaaatcatttttccaaaataacacatttttataccttaatgctgttaagtggttaatgcgt-gtactgtattggtattttgtgtacatttc--agTTATGATCTCAATGTCGATTTGCTGGATGTCCATGCTGACAAGAATACATTTCACCGATTCGACAAGTTCAACTTGAAGTATAATCCTTGTGGCCAGAGT

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S307_76V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------------------------------------------------gtgtgttttgagagcttggattttatcctatgtttatactttatataatgatgga---accactatttagt-tgattatcaattcttcgttttctttttctagGTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGT
                                                                                    |      |    | ||| || | |       | | |  |||  |  |||    |   |  | ||| || | || | ||  ||   |   |   |  |   || ||||| || ||||| || ||  | ||||| ||||  |||||||  ||||| || |||||||| || |||||||||||||||||||| || |||||||| 
gtaagcagatccatgagattaacttaaaccatcatctttgaatatatatatatatatataagataagcattgaccttgatctattacaaactacaggattgaatataaattccaatatgtggtttgaagtatgcaaaatagataattatataatgtggtgatacatatatatgtgcatggtaacagTTATGATTTAAATGTAGACTTGTTGGATGTTCATGTTGACAAAAACACATTCCACCGTTTTGATAAGTTCAACCTTAAGTACAATCCATGCGGCCAAAGC

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|58656752|gb|CK045432.1|CK045432
EST:     GGCACTTATATGACTCTGAAGGAGGTTTTTGAGAGCTTGGACTTAACTGG                         GTATGACTTGAATGTGGATTTACTAGATGTCCATGCGGACAAAAGTACATT
genomic: GGCACTTATATGACTCTGAAGGAGGTTTTTGAGAGCTTGGACTTAACTGGgtgtgttttg ... ctttttctagGTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATT
EST: gi|29638452|gb|CB643461.1|CB643461
EST:     GGCACTTATATGACTCTGAAGGAGGTTTTTGAGAGCTTGGACTTAACTGG                         GTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATT
genomic: GGCACTTATATGACTCTGAAGGAGGTTTTTGAGAGCTTGGACTTAACTGGgtgtgttttg ... ctttttctagGTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATT
EST: gi|29637474|gb|CB642483.1|CB642483
EST:     GGCACTTATATGACTCTGAAGGAGGTTTTTGAGAGCTTGGACTTAACTGG                         GTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATT
genomic: GGCACTTATATGACTCTGAAGGAGGTTTTTGAGAGCTTGGACTTAACTGGgtgtgttttg ... ctttttctagGTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATT

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: 67 (upstream exon), 58 (downstream exon)
Score: 21

GTTGTCATTTTCAGAGACGGCACTTATATGACTCTGAAGGAGGTTTTTGAGAGCTTGGACTTAACTGGgtgtgttttg ... ctttttctagGTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatgatggaaccactatttagttgattatcaattcttcgttttctttttctagGTATGACTTGAATGTTGATTTACTAGATGTCCATGCGGACAAAAGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGT
                     agttgat  putative branch site (score: 21)
                              tcaattcttcgttttc  putative PPT
                tatttagttgattat  TA-rich tract