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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtgatcacttcttgttcatgcaactataaatgtgtagtgttgagtgatgtagtcatgtgatactgcattatcatagaactatcactttgttaattctagaaaacttcacgtgccgcaacattatctgttctagcccccttttccttctgcaaactctgatttgcagttgtcctcacaccaacgctttgtttgctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g65090.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G400604_T01 (Zea mays), 5'ss of exon 7
GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtgat-cacttcttgttca-tgcaactataaatgtgtagtgttgagtgatgtagtcatgtgatactgcattatca-tagaactatcactttgttaattctagaaaacttcacgtgccgcaacattatctgttctagcccccttttccttctgcaaactctgatttgcagttgtcctcacaccaacgctttgtttgctgcag
||||||||||||||||| ||||| ||||| |||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||  |  ||| | | || ||   || ||  | |    |||| |  | |  ||| ||||| ||||||| |   | || |||||  | ||||| |  ||                                                                                                      
GCTTTTGCAATGACGGGTTGGCGTCTTGGTTACCTTGCAGCCCCTAAACATTTTGTTGCAGCATGTGGAAAGATCCAAAGCCAGgtgaaacgattcatttccagtgtttctttatctctaatatgttaaa-ggttaagtgatgtggtactgcacttctagtaaaactaata-tttgtaagatcgtc---------------------------------------------------------------------------------------------------

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA18G02250.1 (Glycine max), 5'ss of exon 7
GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtgatcacttcttgttcatgcaactataaatgtgtagtgttgagtgatgtagtcatgtgatactgcattatcatagaactatcactttgttaattctagaaaacttcacgtgccgcaacattatctgttctagcccccttttccttctgcaaactctgatttgcagttgtcctcacaccaacgctttgtttgctgcag
 | ||||||||||| || ||||| ||||| ||  ||||    |||||||||||||||||||| |  |||||||| ||||||||||| || |  | || || ||     | |   |||| | | | |    |   |   || | | ||| |  | |       || |  ||     |  |||| | |  | |                                                                                           
ACATTTGCAATGACTGGTTGGCGGCTTGGGTATATTGCTTGTCCAAAACATTTTGTTGCAGCATTCGGAAAGATTCAAAGCCAGgt-atgatgtattttttatttcctttt---tgtgaattat-gcacaactca---atatcaaacttc--tcttgatttccttttcctccaagacatctaaacagatgctta----------------------------------------------------------------------------------------

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA08G14720.1 (Glycine max), 5'ss of exon 7
GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtg-atcacttcttgttcatgcaactataaatgtgtagtgttgagtgatgtagtcatgtgatactgcattatcatagaactatcactttgtta-attctagaaaacttcacgtgccgcaacattatctgttctagcccccttttccttctgcaaactctgatttgcagttgtcctcacaccaacgctttgtttgctgcag
|| ||||||||||| || ||||| ||||||||  |||| |  |||||||||||||||||||| ||||||||||||||||| |||||     || | || |    || ||| |    ||  ||  ||     ||  |   ||   ||  | |||| |  ||    | ||  |||| || || ||  |  || ||                                                                                           
GCCTTTGCAATGACTGGTTGGCGGCTTGGATATATTGCTGGTCCAAAACATTTTGTTGCAGCATGTGGAAAGATCCAAAGTCAGgtatgctacattttttattggccacttt---cgta-agccttaccctatacaagtatac-atcatacattttttta----tttccttttgctacatcctccatgacatc-------------------------------------------------------------------------------------------

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA11G36190.1 (Glycine max), 5'ss of exon 7
GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtgatcacttcttgttcatgcaactataaatgtgtagtgttgagtgatgtagtcatgtgatactgcattatcatagaactatcactttgttaattctagaaaacttcacgtgccgcaacattatctgttctagcccccttttccttctgcaaactctgatttgcagttgtcctcacaccaacgctttgtttgctgcag
 | ||||||||||| || ||||| ||||| ||  |||| |  ||||||||||||||||| || |||| |||||| ||||||||||| ||    | || | | |     | |   ||| ||      | ||| ||  | || |  |  |||   |  | | ||     | ||   |  | | | |                                                                                                  
ACATTTGCAATGACTGGTTGGCGGCTTGGGTATATTGCTGGTCCAAAACATTTTGTTGCTGCATGTGAAAAGATTCAAAGCCAGgt-atgctgtattttccgtttccatttttttgtttatgcacaactgaagtttttatttccttttgctccaatacataatagatatttaagttttaccatat-------------------------------------------------------------------------------------------------

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA11G36200.1 (Glycine max), 5'ss of exon 8
GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgt--gatcacttcttgttcatgcaactataaat-gtgtagtgttgagtgatgtagtcatgtga--tactgcattatcatagaactatcactttgttaattctagaaaacttcacgtgccgcaacattatctgttctagcccccttttccttctgcaaactctgatttgcagttgtcctcacaccaacgctttgtttgctgcag
 | ||||||||||| || ||||| ||||| ||| |||| |   ||||||||||||||||||| || |||||||| ||||| |||||  ||| | || || ||        | | |||  || |    | | |     | |  | |    | ||   |  ||  |||  | | | || | |  ||                                                                                                       
ACATTTGCAATGACTGGTTGGCGGCTTGGGTACATTGCTGGTACAAAACATTTTGTTGCAGCATGCGGAAAGATTCAAAGTCAGgtatgatgaatttttatttccatttttgtgaattatgcacaactcaatatcaaacttctcttgatttctttttcctccaagacatctaaattagatgctt-------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA05G31490.1 (Glycine max), 5'ss of exon 6
GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtg-atcacttcttgttcatgcaactataaatgtgtagtgttgagtgatgtagtcatgtgatactgcattatcatagaactatcactttgttaattctagaaaacttcacgtgccgcaacattatctgttctagcccccttttccttctgcaaactctgatttgcagttgtcctcacaccaacgctttgtttgctgcag
|| ||||||||||| || ||||| ||||||||  |||| |  |||||||||||||||||||| ||||||||||||||||| |||||     || | || |    |  ||| |   |    ||  ||     ||  | |||| |          | || |       |     |      || |  | |  | ||                                                                                         
GCCTTTGCAATGACTGGTTGGCGGCTTGGATATATTGCTGGTCCAAAACATTTTGTTGCAGCATGTGGAAAGATCCAAAGTCAGgtatgctacattttttattggtcactttctttcgtaagccttaccctataca-tcatata---------tgtcttgatttccttttcctacagcctccatgacatcttac-----------------------------------------------------------------------------------------

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv18s0001g04860.t01 (Vitis vinifera), 5'ss of exon 7
GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtgatcacttcttgttcatgcaactataaatgtgtagtgttgag--tgatgtagtcatgtgatactgcattatcatagaactatcactttgttaattctagaaaacttcacgtgccgcaacattatctgttctagcccccttttccttctgcaaactctgatttgcagttgtcctcacaccaacgctttgtttgctgcag
 ||||||||||||| || ||||||||||||||||| || |  |||||||| ||||| ||||| |||||||| || || |||||||| ||||     |   | | | |    ||||        |  |   |||   | | |    |||    | |     |   |  | | |     | |  |                                                                                                     
ACTTTTGCAATGACTGGTTGGCGACTTGGATACCTAGCTGGTCCAAAACACTTTGTGGCAGCATGTGGAAAAATTCAGAGCCAGgtaatcatcatctccacctactaaaccaaattctccccttccacattgagaaaatgaataaataaataaatgctgcaaggcagttattacccaagtaatg----------------------------------------------------------------------------------------------------

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|29686132|gb|CB682407.1|CB682407
EST:     TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG                         TTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
genomic: TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtgatcactt ... tttgctgcagTTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
EST: gi|428197|gb|D24345.1|D24345
EST:     TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGNAAGATCCAAAGCCAG                         TTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
genomic: TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtgatcactt ... tttgctgcagTTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
EST: gi|29644554|gb|CB649561.1|CB649561
EST:     TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG                         TTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
genomic: TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtgatcactt ... tttgctgcagTTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
EST: gi|29644410|gb|CB649417.1|CB649417
EST:     TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG                         TTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
genomic: TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtgatcactt ... tttgctgcagTTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
EST: gi|86849106|gb|CI295847.1|CI295847
EST:     TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG                         TTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
genomic: TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtgatcactt ... tttgctgcagTTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
EST: gi|29683532|gb|CB679807.1|CB679807
EST:     TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG                         TTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
genomic: TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtgatcactt ... tttgctgcagTTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
EST: gi|87016653|gb|CI275655.1|CI275655
EST:     TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG                         TTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
genomic: TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtgatcactt ... tttgctgcagTTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
EST: gi|29679352|gb|CB675627.1|CB675627
EST:     TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAG                         TTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG
genomic: TTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtgatcactt ... tttgctgcagTTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTG

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: 70 (upstream exon), 71 (downstream exon)
Score: 23

GCTTTTGCAATGACGGGCTGGCGACTTGGATACCTTGCAGCCCCAAAACATTTTGTTGCAGCCTGTGGAAAGATCCAAAGCCAGgtgatcactt ... tttgctgcagTTTACTTCAGGTGCTAGTAGCATATCACAGAAGGCAGGGCTCGCTGCTTTGAACCTTGGCTACGCTGGTGGTGAAGCAGTCTCAACTATGGTCAAAGCAT




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