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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacagtcatttgatgatttcttactctatttttcagagagtgtgtacagtcactacattctggatcatctattaattgtttccttgtaaatgtttttcatctaccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT

Basic information

species Oryza sativa
transcript LOC_Os01g49690.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 7
gtatgtacagtcatttgatgatttcttactctatttttcagagagtgtgtacagtcactacattctggatcatctattaattgtttccttgtaaatgtttttcatctaccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT
                                 || |    |  ||  |   | |      ||| |||||  | | || ||| | |||||||  ||||      | | ||   |||||||||||  | |||||  | |||| ||||||||||| |||||||||||||| ||||||||||||||||||||||| ||||| || |||||||| |||
-------------------------------gtttgtatgcaatgtaggcttatttttattattatggattgtttttttattctctccttgtggatgtcacct-tttgcca--tgcagTTCAACTTTGTTAACGGTATCGAGCTAGTTTGCCGGGCTCACCAGCTGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTCACT

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G518717_T03 (Zea mays), 3'ss of exon 3
gtatgtacagtcatttgatgatttcttactctatttttcagagagtgtgtacagtcactacattctggatcatctattaattgtttccttgtaaatgtttttcatctaccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT
                                | | | ||     |   | || | | ||  | || |||  | | ||| ||| | | |||| |||||      | | |  | |||||||||||  | ||||   | |||| ||||||||||| |||||||||||||| ||||||||||||||||||||||| ||||| || ||||||||||||
-----------------------------gtgagtatacaatctataatttcatttatta--tccttgattgttt-ttatttgctac-ttgtgaatgtcacct-tttgc--tatgcagTTCAACTTTGTTAATGGTATCGAGCTAGTTTGCCGGGCTCACCAGCTGGTCCAGGAAGGCTTAAAGTACATGTTCCAGGAGAAGGGCCTTGTAACT

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 7
gtatgtacagtcatttgatgatttcttactctatttttcagagagtgtgtacagtcactacattctggatcatctatta-attgtttccttgtaaatgtttttcatctaccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT----
                                     | |   | | | |    | | | | ||  | ||    |||||  || |   |||   | ||     |||     |  |||||||||| || || || || || ||||| ||||| ||||| ||||| || |||||||||||| | ||||| ||||| || || |||||||||||||||    
------------------------------------gtaatgtaatttatttgttaattgcttttagaattgaatattatgttttaatcttaccagtg-----cattcttttcatgcagTTCAATCACATAAATAACCTTGATCTTGTTTGTCGAGCGCACCAACTCGTTCAGGAAGGCCTTAAGTATATGTTCCAAGATAAAGGCCTTGTAACTGTAT

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G23310.1 (Glycine max), 3'ss of exon 7
gtatgtacagtcatttgatgatttcttactctatttttcagagagtgtgtacagtcactacattctggatcatctatta-attgtttccttgtaaatgtttttcatctaccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT
                                     | |   | | | |    | | | | ||  | ||    |||||  || |   |||   | ||     |||     |  |||||||||| || || || || || ||||| ||||| ||||| ||||| || |||||||||||| | ||||| ||||| || || |||||||||||||||
------------------------------------gtaatgtaatttatttgttaattgcttttagaattgaatattatgttttaatcttaccagtg-----cattcttttcatgcagTTCAATCACATAAATAACCTTGATCTTGTTTGTCGAGCGCACCAACTCGTTCAGGAAGGCCTTAAGTATATGTTCCAAGATAAAGGCCTTGTAACT

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 7
gtatgtacagtcatttgatgatttcttactctatttttcagagagtgtgtacagtcactacattctggatcatctattaattgttt-ccttgtaaatgtttttcatctaccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT
                                 |  | |  |  |||  |    | | |  |||  | ||     ||||  |||     ||  |||||  ||   |  |     ||||||||||  | || |||||||| ||||| ||||| || || ||||| || ||||| |||||  | ||||| ||||| ||||| |||||||||||||||
--------------------------------gtaatgccaattgtgaat-tgcttattgaattgagtattgaacattatgtgtgaattttacaaatgccttgttttca-----tgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 7
gtatgtacagtcatttgatgatttcttactctatttttcagagagtgtgtacagtcactacattctggatcatctattaattgtttccttgtaaatgtttttcatctaccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT
                                     | |   | | | |    | | | | ||  | ||    |||   || |   |||   |     || |||     |  | |||||||| || || || || || ||||| ||||| ||||| ||||| || |||||||||||| | ||||| ||||| || || |||||||||||||||
------------------------------------gtaatgtaatttatttgttaattgcttttagaattgaatat--gttttaatcttacca-----ttgcattcttttcatacagTTCAATCACATAAATAACCTTGATCTTGTTTGTCGAGCACACCAACTCGTTCAGGAAGGCCTTAAGTATATGTTCCAAGATAAAGGCCTTGTAACT

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G43470.1 (Glycine max), 3'ss of exon 7
gtatgtacagtcatttgatgatttcttactctatttttcagagagtgtgtacagtcactacattctggatcatctatta-attgtttccttgtaaatgtttttcatctaccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT
                                     | | | | | | |    | | | | ||  |  |    |||||   | |   |||   | ||     |||     |  |||||||||| || || || ||||| ||||| ||||| ||||| ||||| || ||||| |||||| | ||||| ||||| || || |||||||||||||||
------------------------------------gtaatataatttatttgttaattgcttttagatttgaatattatgctttaatcttaccagtg-----cattcttttcatgcagTTCAATCACATAAATAATCTGGATCTTGTTTGTCGAGCACACCAACTCGTTCAAGAAGGCCTTAAGTATATGTTCCAAGATAAAGGCCTTGTAACT

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatgtacagtcatttgatgatttcttactctatttttcagagagtgtgtacagtcactacattctggatcatctattaattgtttccttgtaaatgtttttcatctaccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT
        | | || |  |  | |     |  | |||  | |  ||||| | ||  |  |           || ||||    ||| |||  |   || ||||  |    ||| ||||||| ||||||||||||||||| |||||||| || || ||||||||||| || || |||||  | ||||||||||| || || ||||| |||||||||
------gtatttatatttttttctggggttgaaatttgaataaggtgtgaaaagaaataa-----------atgtattt-cagttccctgatctgtggttttgctt---cttgtgcagTTTAACCATATTAACAATCTTGATCTAGTATGTCGCGCTCACCAGCTTGTACAAGAAGGTCTCAAGTACATGTTCCAAGATAAAGGTCTTGTAACT

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatgtacagtcatttgatgatttcttactctatttttcagagagtgtgtacagtcactacattctggatcatctattaattgtttccttgtaaatgtttttcatctaccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT
                         |   | || |||    | ||  || |  |  |||  |  ||     ||  |||     | || |  |   || || |    |  ||| ||||||| |||||||| ||||| || |||||||| ||||| || ||||| || || || |||||  | ||||||||||| || || |||||||||||||||
------------------------gtatgtttactttctcaaaagcttgaattgatactgtaa-ctaagaaattaatttcacatctc-tgatctttggttctggctt--cttgtgcagTTTAACCATATCAACAAGCTGGATCTAGTATGCCGCGCGCACCAACTTGTACAAGAAGGTCTTAAGTACATGTTCCAAGATAAAGGCCTTGTAACT

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 3'ss of exon 7
gtatgtacagtcatttgatgatttcttactctatttttcagagagtgtgtacagtcactacattctggatcatctattaattgtttccttgtaaatgtttttcatctaccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT
                                         ||||||  |||| || |  | |  |   |     | |   ||||| ||    ||| |||||  | |    ||| ||||||||||| || |||||||| ||||| ||||| ||||| |||||||| || || |||||  ||||||||||||||||||| ||||| || ||||| 
---------------------------------------gtagagtg-atacaatctcggcttcgtcttttccagacttcatgtttgctgaggaattttttttcttt---ctttacagTTCAACCACATAAACAATCTTGATCTGGTTTGTCGAGCCCACCAGCTTGTACAAGAAGGTCTAAAGTACATGTTTCAGGATAAAGGACTCGTAACC

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|88989163|gb|CI042276.1|CI042276
EST:     TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|86253096|gb|CI058021.1|CI058021
EST:     TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|163921174|gb|EG710163.1|EG710163
EST:     AGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: AGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|218484413|gb|FG953190.1|FG953190
EST:     TTAGCCCTCGTGGAGCAGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|24468838|gb|CA305787.1|CA305787
EST:     TAGCCCTCNGTGGAGCAGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: TAGCCCTC-GTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|27577318|gb|CB000013.1|CB000013
EST:     TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|86870962|gb|CI326781.1|CI326781
EST:     TTAGCCCTCGTGGAGCTGGTT-GCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|431829|gb|D23910.1|D23910
EST:     TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|325493557|gb|JG458081.1|JG458081
EST:     GGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGGTTGCCGAGCTCACCAGCTGGTT
genomic: GGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|218492898|gb|FG955355.1|FG955355
EST:     TTAGCCCTCGTGGAGCAGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|27577630|gb|CB000325.1|CB000325
EST:     TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|86422413|gb|CI059986.1|CI059986
EST:     GGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: GGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|86419470|gb|CI054271.1|CI054271
EST:     CGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: CGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|27334364|gb|CA882815.1|CA882815
EST:     TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAAATCTCGATCTAGTTTTGCCGAGCTCACCAGCTGG
genomic: TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAA-TCTCGATCTAGTTT-GCCGAGCTCACCAGCTGG
EST: gi|51946060|gb|CV152401.1|CV152401
EST:     TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|89180552|gb|CI044831.1|CI044831
EST:     TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
EST: gi|29686455|gb|CB682730.1|CB682730
EST:     TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAG                         TTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT
genomic: TTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTT

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: 74 (upstream exon), 74 (downstream exon)
Score: 58

TTTCTGTGATCTAATGTGGAGTGACCCTGAAGAAATAGAGACATGGGCTGTTAGCCCTCGTGGAGCTGGTTGGCTTTTTGGATCACGAGTGACAGCTGAGgtatgtacag ... ccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctggatcatctattaattgtttccttgtaaatgtttttcatctaccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT
           tattaat  putative branch site (score: 58)
                                  tttttcatctaccttt  putative PPT
        atctattaattgttt  TA-rich tract