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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagtttgattttatctactttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA

Basic information

species Oryza sativa
transcript LOC_Os07g47100.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 6
gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagtttgattttatctactttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
|||  |||||| |  ||||  | |    ||||  |   |    |  | |||   | | |  | |     ||  | | | ||  ||| |||| |||||||| |||| |||||||| |||||||||||||| || || || ||||| |||||||| ||||| || || |||||||| |||||||| ||||| |
gtgcacctctgatcagatgtggcaagggaattcacgcttg---ttgtcttactctcttaactgactctgttcatatatatggcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATGTCGCATTACACCTGGCACAATGTGACAGAGAGCTCAAGAGTCACAACCA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
----------gtgtgcctctgc----tttgatgcagtatcaaaatttgca-tatagtttcattttatagtttgattttatctactttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
            |  | || |     |||  |  |||||     ||||   | ||  |  ||||| |  | |||     | |    | | | |   |  |  ||||||     || |||| |||||||| || |||||||||||||| ||||| ||||| ||||| ||||||||||| || || ||||| || ||| | || || |
gtaagttttaaagaacttcagaaatattttgtagagtatgtctttttgagctctatatctattttttcttgtgaaagggt-tctgatatatctacaagttctgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 8
gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagtttgattttatctactttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
||  |  | | || |||  |     ||   |||   | ||  |   |   ||          || |   ||| ||| |||||      ||| |  |   ||| || | |||||| || || |||||||| || ||||| ||||| || ||||| |||||||| || ||||||||||||||||| ||||| |
gtaagaattttctctgaaacttggccacctttttagtgtaaataattcccatg--------ctaaccgatttatttctttga------cagCTATTTTCTTTAAGTGCCATTCTGACTGTTTTCTTCTGCGGCATTGTTATGTCTCACTACACGTGGCATAATGTGACAGAGAGTTCAAGAGTGACAACCA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G02560.1 (Glycine max), 3'ss of exon 7
gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagtttgattttatctactttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
||  |    | || |||  |   | | |        | |||| | |    | | |   ||  || | | ||| ||| ||||      |||| |  |   ||| || | |||||| || || |||||||| || ||||| ||||| || ||||| |||||||| || ||||||||||||||||| ||||| |
gtaagaaaattctctgaaactcgacccaccacctt-tgtagtgtaaa---aaattccaatgctaaccaatttatttctttg------gcagCTATTTTCTTTAAGTGCCATTCTGACTGTTTTCTTCTGCGGCATTGTTATGTCTCACTACACGTGGCATAATGTGACAGAGAGTTCAAGAGTGACAACCA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
-----------------------gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagtttgattttatctactttgtttgtt-tgatat---tggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
                        |||  || | |  |    |  | |  |  | |  || || |||  | || | ||    |  |   |  ||     ||| ||||||     ||||||     || |||| ||||||||||| |||||||||||||| ||||| ||||| ||||| ||||||||||| || || ||||| || ||| | || || |
gtaagttttaaagaacttcagaaatgt-tctgtacagtatgtcttttttgagctctatatcta-ttttttgttgtggtacattcattaatcattaacgggttctgatatattctgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagtttgattttat-ctactttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
||  |  | |       |  ||||      | || ||   ||     ||| | ||| ||  | || ||  | | | |   |  | ||| |||||     || |||| ||||||||||| |||||||| ||||||||||| ||||| ||||| || ||||||||||| || |||||||||||| | || || |
gtaagt-tgtaaagaattttagtaatgttttatggatgctgtcaacatttgtcgtt-gacatgatgctgatgtatctacatc-tgttg-cagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA20G37370.1 (Glycine max), 3'ss of exon 9
gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagtttgattttatctactttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
||  |  | |       |  ||||      | || ||   |   |||||   |  || |  |   ||  | | | |   |    |  |||||||    || |||| ||||||||||| |||||||| ||||| ||||| ||||| ||||| || |||||||| || || |||||||||||| | || || |
gtaagttt-taaagaattttagtaatgttttatggatgctgcaacatttgtca--ttaacatatgctgatgtatctacat--cttctgcagTTGTCCTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGGATTGTCATGTCTCATTATACCTGGCATAATGTGACTGAGAGTTCAAGAATCACTACCA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 5
----gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcatt---ttatagtttga-----ttttatctactttgt-ttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
    || |        |||    || | ||| |||||    || |   || |   || ||  || |      |||||  |   | | |||||||    | |||| |  | |  ||||| || || || || ||||| |||||||| ||||| ||||| |||||||||||||| || ||||| ||||| |||||| |||| || |
gttagttttgtgaaattttataccactgtcataatttaggcatggagacaatcagttgtatcttaagaatcctttattgataatatattgtttggg--ttgcagCTATTCGCCTTGAGTGGTATCCTAACTGTATTTTTCTGTGGGATTGTGATGTCCCATTACACTTGGCACAATGTCACCGAGAGCTCAAGAATTACTACCA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G27150.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagtttgattttatctactttgt-ttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
||  |  |   |||| |   |  |  || || | |||  |||| ||||  | |     ||| |||  |  || | ||  ||  |  | |||| |  | || |||||||| || ||||| || || |||||||||||||| ||||| |||||||| ||||| || || || ||||| |||||| | |||||||
gttagatt---cttttaaataacacgaacatattcattcagttgcattc-aaacacaaattatattgatgttatattaatt--tggttgcagCTTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 8
-------------------------------------------------------------------------gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagttt---gattttatctactttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
                                                                          |   | ||   ||   |||  ||| |  |||    |||  |    || | |  |||   |||  | | ||     | ||||    ||   |||||| |  |||| || ||||||||||| |||||||| || || ||||| |||||||| ||||| ||||||||||| || || ||||||||||| || ||||
gtaagatttctttctacccttcaagcacctttataagaatctcatcaagttctgtttgaaatatacaaggactatcatcatccaattctgtgctttataaggatta--ttatcatccacttctgtgctttactgatagtgtttataaattctgttcatcatc--cagTTGTTCTATTTAAGTGGCATTCTCACTGTATTCTTTTGCGGGATTGTCATGTCACACTACACCTGGCATAACGTGACTGAAAGTTCAAGAGTCACCACAA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 8
------------------------------------------gtgtgcctctgctttga-tgcagtatcaaaatttgcatatagtttcattttatagtttgattttatctacttt--gtttgtttgatattg--gcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
                                           |||   |  || |||| ||   |||  | |||      ||| |  ||     | ||  | | | || | | |  ||   |||| |  |   |||| |  |  ||||||| ||||||||||| ||||| |||||||| ||||||||||| |||||||| ||||| || || ||||||||||||||||| || || |
gtaagatttcttttaacttcttgggcacttccctggcccctgttgtctattggcattgagtgttctatttagattcaacagtagatatatcaatcatttaaagtctttccattgttagtaactttggttgtcctgcagCTATTCTATTTGAGTGGCATTCTCACGGTATTTTTCTGTGGGATTGTAATGTCCCATTACACGTGGCACAATGTTACAGAGAGTTCAAGAGTCACTACCA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S31_203V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------------------------------------------gtgtgcctctgctttgat-gcagtatcaaaattt----------gcatatagtttcattt--tatagtttgattttatctact-ttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
                                                                         |     |||  ||     ||  | |  ||||||          |  |||  ||| |||   |  |   |||  | || |  | || | ||| |  |    |||| |  |  |  |||| || ||||| ||||| ||||| ||||| |||||||||||||| ||||| |||||||||||||| || || ||| |||| || || |
gtcccccttcctctctctctctctcgactatatgcattgtttggattaaagagtctattagtttctttttaatttcaattctatttcagcagcgttgttgaaatttagtcgctgatgtctattattttattccctgcacgatgaactcatttcgtgttttctgtgtattgcatgcagCTTTTCTACCTGAGTGGAATTCTTACCGTCTTCTTTTGTGGCATTGTAATGTCACACTACACCTGGCATAACGTCACTGAAAGCTCACGAGTAACTACCA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------gtgtgcc-tctgctttgatgcagtatcaaa-atttgcatat-agttt---cattttatagttt----gattttatctactttgttt--gtttga-----tattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
                                                  |  |||  | |   |||| |  | | |    || ||  ||  |||||   ||  || ||  |     | |||||   |  ||  ||  || ||      | || |||| |  |  | ||||| || |||||| | || ||||| || || ||||||||||| ||||||||||||||||||||||| |||| |||  || | ||||  |
gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcatctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtatgcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S113_117V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------gtgtgcctctg----ctttgatgcag-----tatcaaaatttgcatatagtttcattt--tatagtttg----------atttta------tctactttgtttgtttgatattgg--cagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
                                      | ||   |||     ||| |   ||     |    ||||  |||||   |||   ||  || |  |||          |||||       | ||||||      | |  |||||  ||| |  |  | ||||| || || ||| | || ||||| ||||| ||||||||||| ||||||||||||||||| ||||| || | |||  ||   ||||| |
gtcagtttgaccttctatgtggattgttcgtccaattatctgttcctggaatttttcaaatagatcgatgaggaaatgagcatacgatttggattgttacaacttgtaaatctgaaattttcagaaattttactttcgcgtgtcgtcattggtgcagCTTTTCTACTTGAGTGGAATACTCTCAGTGTTCTTTTGTGGCATTGTAATGTCTCATTACACTTGGCATAATGTCACGGAAAATTCTCGAACCACAACCA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ05720 (Selaginella moellendorffii), 3'ss of exon 7
gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagtttgattttatctactttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
                        | | | |||   | | || |       |||  |   ||  | | ||   |  || ||  |||  ||| || |  |  |||| || || ||||| || ||||| ||||| ||||| ||||||||||| || ||||| |||||||| ||||| |||||| | ||||| |
-----------------------gtgatagtttttttct-gtatagagaggtagcatttcttcttgttctc-atgcgtatgccattc-cagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ32893 (Selaginella moellendorffii), 3'ss of exon 7
gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagtttgattttatctactttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
                        | | | |||   | | || |       |||  |   ||  | | ||   |  || ||  |||  ||| || |  |  |||| || || ||||| || ||||| ||||| ||||| ||||||||||| || ||||| |||||||| ||||| |||||| | ||||| |
-----------------------gtgagagtttttttct-gtatagagaggtagcatttcttcttgttctc-atgcgtatgccattc-cagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA

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|27549114|gb|CA767092.2|CA767092
EST:     AGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG                         TTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATG
genomic: AGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAGgtgtgcctct ... atattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagtttcattttatagtttgattttatctactttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
                                        gtttgat  putative branch site (score: 5)
     tttcattttatagttt  TA-rich tract