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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGCTTCTAAAAAAGCTCAAGGGAGCACAGTGCATCCATCAACTCACTTTCAGTGATGATCAAGACCCCCAGAATACATTCTTTTATAAACTTTGTAAGgtatggtatcaccctctgcttcgttctgtagtgcattcagtaatcctatctgttgcgaatttatatcagatcttagaattggccataagctgttcccttttataatccttttcag

Basic information

species Oryza sativa
transcript LOC_Os12g06800.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G127810_T02 (Zea mays), 5'ss of exon 3
CTGGCTTCTAAAAAAGCTCAAGGGAGCACAGTGCATCCATCAACTCACTTTCAGTGATGATCAAGACCCCCAGAATACATTCTTTTATAAACTTTGTAAGgtatggtatcaccctctgcttcgttctgtagtgcattcagtaatcctatctgttgcgaatttatatcagatcttagaattggccataagctgttcccttttataatccttttcag
|||||| || ||||||||||||   || || ||||||||||||||||||||||||||||||||||||||||| ||||||| ||| ||||| ||||| ||||||     || | ||    |   |      || ||    ||       | ||        |  | |||       |||||  |  | | || || |  ||| |  || |   |||
CTGGCTGCTGAAAAAGCTCAAGAATGCTCAATGCATCCATCAACTCACTTTCAGTGATGATCAAGACCCCCACAATACATACTTCTATAAGCTTTGCAAGgtaccaagtctctctagagtaactcagaccgttcaactcgttgctgattttgccatattctattttcatcaagatgaatttacatttaactattgctatttttgttcat--acag

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G176042_T02 (Zea mays), 5'ss of exon 7
CTGGCTTCTAAAAAAGCTCAAGGGAGCACAGTGCATCCATCAACTCACTTTCAGTGATGATCAAGACCCCCAGAATACATTCTTTTATAAACTTTGTAAGgtatggtatcaccctctgcttcgttctgtagtgcattcagtaatcctatctgttgcgaatttatatcagatcttagaattggccataagctgttcccttttataatccttttcag
|||||| || ||||||||||||   || || ||||||||||||||||||||||||||||||||||||||||| ||||||| ||| ||||| ||||| ||||||     || | ||    |   |      || ||    ||       | ||        |  | |||       |||||  |  | | || || |  ||| |  || |   |||
CTGGCTGCTGAAAAAGCTCAAGAATGCTCAATGCATCCATCAACTCACTTTCAGTGATGATCAAGACCCCCACAATACATACTTCTATAAGCTTTGCAAGgtaccaagtctctctggagtaactcagaccgttcaactcgttgctgattttgccatattctattttcatcaagatgaatttacatttaactattgctctttttgttcat--acag

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G039505_T01 (Zea mays), 5'ss of exon 12
CTGGCTTCTAAAAAAGCTCAAGGGAGCACAGTGCATCCATCAACTCACTTTCAGTGATGATCAAGACCCCCAGAATACATTCTTTTATAAACTTTGTAAGgtatggtatcaccctctgcttcgttctgtagtgcattcagtaatcctatctgttgcgaatttatatcagatcttagaattggccataagctgt-tcccttttataatccttttcag
|||||| || |||||||||||||| || || ||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| ||||| ||||||    ||| |   |    | |  ||| | |   ||  |  || | |  ||||||   ||| |  ||| | ||    ||      ||||||  |   |  || |           
CTGGCTGCTGAAAAAGCTCAAGGGTGCGCAATGCATCCATCAACTCACTTTCAGTGATGATCAAGACCCCCAGAATACATACTTTTATAAGCTTTGCAAGgtacaaaatctctgccc---tggccctggactaacttgggccattcaacttgttgctggtttctgccagtttttttt-ttaatatcaagctgaatttatcatacag----------

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G468799_T01 (Zea mays), 5'ss of exon 12
CTGGCTTCTAAAAAAGCTCAAGGGAGCACAGTGCATCCATCAACTCACTTTCAGTGATGATCAAGACCCCCAGAATACATTCTTTTATAAACTTTGTAAGgtatggtatcaccctctgcttcgttctgtagtgcattcagtaatcctatctgttgcga---atttatatcagatcttagaattggccataagctgttcccttttataatccttttcag
|||||| || ||||||||||||   || || ||||||||||||||||||||||||||||||||||||||||| ||||||| ||| ||||| ||||| ||||||     || | ||    |   |      || ||    ||       | ||         ||||| ||||       |||||  |  | | || || |  ||| |  || |   |||
CTGGCTGCTGAAAAAGCTCAAGAATGCTCAATGCATCCATCAACTCACTTTCAGTGATGATCAAGACCCCCACAATACATACTTCTATAAGCTTTGCAAGgtaccaagtctctctggagtaactcagaccgttcaactcgttgctgattttgccatattctatttacatcaagat---gaatttacatttaactattgcactttttgttcat--acag

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G163594_T01 (Zea mays), 5'ss of exon 8
CTGGCTTCTAAAAAAGCTCAAGGGAGCACAGTGCATCCATCAACTCACTTTCAGTGATGATCAAGACCCCCAGAATACATTCTTTTATAAACTTTGTAAGgtatggtatcaccctctgcttcgttctgtagtgcattcagtaatcctatctgttgcgaatttatatcagatcttagaattggccataagctgttcccttttataatccttttcag
|||||| || ||||||||||||   || || ||||||||||||||||||||||||||||||||||||||||| |||||||  || ||||| ||||| ||||||     || | ||    |   |      || ||    ||       | ||        |  | |||       |||||  |  | | || || |  ||| |  || |   |||
CTGGCTGCTGAAAAAGCTCAAGAATGCTCAATGCATCCATCAACTCACTTTCAGTGATGATCAAGACCCCCACAATACATATTTCTATAAGCTTTGCAAGgtaccaagtctctctggagtaactcagaccgttcaactcgttgctgattttgccatattctattttcatcaagatgaatttacatttaactattgctctttttgttcat--acag

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA06G09480.1 (Glycine max), 5'ss of exon 14
CTGGCTTCTAAAAAAGCTCAAGGGAGCACAGTGCATCCATCAACTCACTTTCAGTGATGATCAAGACCCCCAGAATACATTCTTTTATAAACTTTGTAAGgtatggtatcaccctctgcttcgttctgtagtgcattcagtaatcctatctgttgcgaatttatatcagatcttagaattggccataagctgttcccttttataatccttttcag
 ||| |||| || ||||| || ||  |||||||||| ||||||||||||||||  ||||||| |||   ||| ||||||||  | |||||||| ||||||||| || ||      || |   | |    | |  | | ||  |  | ||    |   | | | |    | |   | ||       |  | ||| |  |||   ||          
GTGGTTTCTGAAGAAGCTAAAAGGCACACAGTGCATTCATCAACTCACTTTCACAGATGATCCAGATTTCCAAAATACATTTCTCTATAAACTGTGTAAGgta-gggattgtgtcctacaatggttg--aataaaatgagacagac-atgaactattagtct-tgcttgcttgaataacctattgtgggatgtactttttaccaa----------

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|58597607|gb|CK008135.1|CK008135
EST:     TCAGTGATGATCAAGACCCCCAGAATACATTCTTTTATAAACTTTGTAAG                         TTGAAGACACTGGAGAACTTCAAAAATATTATACTTCTATCTTCACCACAG
genomic: TCAGTGATGATCAAGACCCCCAGAATACATTCTTTTATAAACTTTGTAAGgtatggtatc ... tccttttcagTTGAAGACACTGGAGAACTTCAAAAATATTATACTTCTATCTTCACCACAG
EST: gi|29613529|gb|CB618542.1|CB618542
EST:     CCCAGAATACATTCTTTTATAAACTTTGTAAG                         TTGAAGACACTGGAGAACTTCAAAAATATTTATACTTTCTATCTTCACCAC
genomic: CCCAGAATACATTCTTTTATAAACTTTGTAAGgtatggtatc ... tccttttcagTTGAAGACACTGGAGAACTTCAAAAATA-TTATAC-TTCTATCTTCACCAC
EST: gi|33381178|gb|CF196521.1|CF196521
EST:     TCAGTGATGATCAAGACCCCCAGAATACATTCTTTTATAAACTTTGTAAG                         TTGAAGACACTGGAGAACTTCAAAAATATTATACTTCTATCTTCACCACAG
genomic: TCAGTGATGATCAAGACCCCCAGAATACATTCTTTTATAAACTTTGTAAGgtatggtatc ... tccttttcagTTGAAGACACTGGAGAACTTCAAAAATATTATACTTCTATCTTCACCACAG

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: 69 (upstream exon), 58 (downstream exon)
Score: 11

CTGGCTTCTAAAAAAGCTCAAGGGAGCACAGTGCATCCATCAACTCACTTTCAGTGATGATCAAGACCCCCAGAATACATTCTTTTATAAACTTTGTAAGgtatggtatc ... tccttttcagTTGAAGACACTGGAGAACTTCAAAAATATTATACTTCTATCTTCACCACAG




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