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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_Os07g47100.1
intron # 9
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




















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: 67 (upstream exon), 71 (downstream exon)
Score: 13

GCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAGgtgtgcctct ... atattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagtttcattttatagtttgattttatctactttgtttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
                                        gtttgat  putative branch site (score: 13)
     tttcattttatagttt  TA-rich tract