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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcacagttctagtcttgcccactccagatcttgtgtatgtgtgtatgcacactaaaatatctgtactttcacactgatcatgaagtcatgtaacatcttgtctgcacatgtttctggattttgcagATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTAT

Basic information

species Oryza sativa
transcript LOC_Os12g06810.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 8
gtaattcacagttctagtcttgcccactccagatcttgtgtatgtgtgtatgcacactaaaatatctgtactttcacactgatcatgaagtcatgtaacatcttgtctgcacatgtttctggattttgcagATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTAT
                    |   ||| | || |||    | |         | | ||   || |  | |      |  || |    ||||    | ||||| |   | || || ||| |  | |||||||| |||||||||| ||||||||||| ||| |||||||||||||||||||||||||||| || ||||| ||||||||||||||| | ||| ||||||| || 
-------------------gtaaacacac-agctctaacatctcaaccatctccctctctcatgttagcataaatgctgtggt----aagtt---tgacatcatagatacatatttttatttactttgcagACTATGGGATCTAGGACAGCAGCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTAC

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA19G43070.1 (Glycine max), 3'ss of exon 8
gtaattcacagttctagtcttgcccactccagatcttgtgtatgtgtgtatgcacactaaaatatctgtactttcacactgatcatgaagtcatgtaacatcttgtctgcacatgtttctggattttgcagATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTAT
                                     ||  |||     ||    | | | |    | |   ||     || |  ||  ||    ||| |   |||| |    ||||||       |  ||  | |||||| | || |||||| ||||| | ||||||||||| || ||||| ||||| || ||||| ||||| ||||| ||  | |||||||||||||||
-------------------------------------gta-atgcacacatatggagttataagcatttctatttgttttgtttttgtggttgactaataatctgtcgg----tgtttcc------tctagGCTTTGGGATATAGGTCAGCAGAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTAT

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G30050.1 (Glycine max), 3'ss of exon 7
gtaattcacagttctagtcttgcccactccagatcttgtgtatgtgtgtatgcacactaaaatatctgtactttcacactgatcatgaagtcatgtaacatcttgtctgcacatgtttctggattttgcagATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTAT
                                       |||  || || |  |   |   |||    || ||||    || |       | |||    | ||  |||   ||| ||||      |   ||  | |||||||| || ||||| || ||| | ||||||||||| || ||||| |||||  | ||||| |||||||||||| |  | |||||||||||||||
---------------------------------------gta-atgcgtgtatatggttttata---ataatttctttttgtt-------ttatggttta-ctaatctcaccatctttca-----tcatagGCTTTGGGATCTTGGTCAGCAACGCTGTGTGCATTCTTATGCAGTTCATACAGATTCTATTTGGGCTCTTGCAAGCACTTCAACATTTAGTCATGTTTAT

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA19G42990.1 (Glycine max), 3'ss of exon 8
gtaattcacagttctagtcttgcccactccagatcttgtgtatgtgtgtatgcacactaaaatatctgtactttcacactgatcatgaagtcatgtaacatcttgtctgcacatgtttctggattttgcagATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTAT
                                   |  || |    | |      | ||  || |||||   ||     |  |  ||   |    ||| |   ||||    ||  ||||      |   ||  | |||||| | || |||||  ||||| | ||||||||||| || ||||| ||||| || ||||| ||||| ||||| ||  | |||||||||||||||
----------------------------------gtaatgcacacatatggagttattaccatttctgtttgttttgttttgttttgtgtttgactaataatctgtc----caactttcc-----tcatagGCTTTGGGATATAGGTCAGCAAAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTAT

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA03G40360.1 (Glycine max), 3'ss of exon 8
gtaattcacagttctagtcttgcccactccagatcttgtgtatgtgtgtatgcacactaaaatatctgtactttcacactgatcatgaagtcatgtaacatcttgtctgcacatgtttctggattttgcagATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTAT
                                       |||    || |  || |   |  |||    | ||         |  |   ||  | | ||   |  ||||  ||| ||||      |   ||  | |||||| | || |||||| ||||| | ||||||||||| || ||||| ||||| || ||||| ||||| ||||| ||  | |||||||||||||||
---------------------------------------gta---atgcacacatatggagttattaccatttctgtttgttttgttttgt-gtttgactaataatctgtccatctttcc-----tcatagGCTTTGGGATATAGGTCAGCAGAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTAT

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G05090.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaattcacagttctagtcttgcccactccagatcttgtgtatgtgtgtatgcacactaaaatatctgtactttcacactgatcatgaagtcatgtaacatcttgtctgcacatgtttctggattt---tgcagATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTAT
                                               || || |   |      |||  |||   ||| | |  ||||   | || | ||| |    |  |  || ||||  |||    |  ||| |||||||||| || |||||||||||| ||||| | ||||| |||||||| ||||| || |||||||||||| |||  || || |||||||||||||||
-----------------------------------------------gtctgtatttt------tcttaactagtaca-taactatgatagc-tgaatcatttcagttctaactggttctaaattcatgtttagACTATGGGATCTAGGTCAGCAGCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTAT

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 8
gtaattcacagttctagtcttgcccactccagatcttgtgtatgtgt-gtatgcacactaaaatatctgtactttcacactgatcatgaagtcatgtaacatcttgtctgcacatgtttctggattttgcagATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTAT
                         |   |  ||    | ||||| | || |     || | | ||   | |||| |      |||||  ||     | || | ||  | ||  | | |    ||||  |||  |||||||||| || |||||| ||||  | ||||| ||||| |||||||| ||||| |||||||| ||||||||||| ||  | ||||| |||||||||
-------------------------atcacgcattcaatatatgtttcgtttatttccttata-attaatcctttta-gtgcttcatgtggttg---atcaacctg--tacatctctcttcacatttcacagGCTATGGGATCTTGGTCAGCAGAGATGCGTGCATTCCTATGCCGTGCATACAGATTCTGTCTGGGCACTTGCAAGCACCCCAACATTTAGCCATGTTTAT

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S69_10V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaattcacagttctagtcttgcccactccagatcttgtgtatgtgtgtatgcacactaaaatatctgtactttcacactgatcatgaagtcatgtaacatcttgtctgca----catgtttctggattttgcagATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTAT
                                || | ||     |     | |||  | ||| ||   | ||  |  | || |  | || |  | |  |  ||  |  | |    | | |||    | | |||||  | |||||| | ||||| || || || |||||||||||||| || ||||| ||||| |||||||| ||||||||||| ||||| || ||||| || |||
--------------------------------atttggtaaggttaatattccacgttgaaacattcttcct--cgtagtggttgt-aatttttcttcctactcattagaagtcccttattttcataatatgcagGCTTTGGGATTTAGGACAACAACGCTGCATTCATTCTTATGCAGTTCATACAGATTCTGTCTGGGCTCTTGCAAGCACGCCTTCCTTCAGTCACGTGTAT

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|29678630|gb|CB674905.1|CB674905
EST:     GTATTGTCTTTCAGGCTCATCTGATTCAATGATAAG                         ATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATAC
genomic: GTATTGTCTTTCAGGCTCATCTGATTCAATGATAAGgtaattcaca ... gattttgcagATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATAC
EST: gi|29670913|gb|CB667188.1|CB667188
EST:     GTATTGTCTTTCAGGCTCATCTGATTCAATGATAAG                         ATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATAC
genomic: GTATTGTCTTTCAGGCTCATCTGATTCAATGATAAGgtaattcaca ... gattttgcagATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgatcatgaagtcatgtaacatcttgtctgcacatgtttctggattttgcagATTATGGGATCTGGGACAGCAGCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTAT
                atgtaac  putative branch site (score: 3)
                                              atttt  TA-rich tract