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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaagtggtctttctcatgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTGCAAGGACTCTGTAAACATAGATGTTGTCATTGATTGGCTTATCAAGCAC

Basic information

species Oryza sativa
transcript LOC_Os02g49980.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g49980.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G089454_T01 (Zea mays), 3'ss of exon 5
gtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaagtggtctt---tctcatgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTGCAAGGACTCTGTAAACATAGATGTTGTCATTGATTGGCTTATCAAGCAC
||||| | | | | |  | ||  |  ||   |||| ||         | || ||| || ||  |||| ||||||   | ||   | |  ||| |||||| || ||||||| |||||||||||| |||||||| |||||||||||||| |                                                  
gtgagctcaat-cttcatttgcctacgc--atcattct---------actttctgcattataattcagctgaagctcttttgacttttttgt-tttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCT--------------------------------------------------

upper sequence: LOC_Os02g49980.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G089454_T03 (Zea mays), 3'ss of exon 4
gtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaagtggtctt---tctcatgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTGCAAGGACTCTGTAAACATAGATGTTGTCATTGATTGGCTTATCAAGCAC
||||| | | | | |  | ||  |  ||   |||| ||         | || ||| || ||  |||| ||||||   | ||   | |  ||| |||||| || ||||||| |||||||||||| |||||||| |||||||||||||| || ||||| ||||| ||||||||  ||||||| || |||||||||||||||
gtgagctcaat-cttcatttgcctacgc--atcattct---------actttctgcattataattcagctgaagctcttttgacttttttgt-tttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTGTAAGGATTCTGTGAACATAGACATTGTCATCGACTGGCTTATCAAGCAC

upper sequence: LOC_Os02g49980.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G171060_T02 (Zea mays), 3'ss of exon 6
gtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaag-----tggtctttctcatgtat---ttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTGCAAGGACTCTGTAAACATAGATGTTGTCATTGATTGGCTTATCAAGCAC
|| || | |  |||||   | ||    ||  | ||  |         | || ||| ||||| | ||| || |||     || ||| |  | | | |   ||||| || ||||||||||||||||||||||| ||||| |||||||||||||| || ||||| ||||| |||||||| || ||||| || |||||||||||||||
gtaagctca--accttcatt-tgcttactcataattat---------actttctgcatgatatctcagctcaagctctctgctctcttccctttttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTGTAAGGATTCTGTGAACATAGACGTCGTCATCGACTGGCTTATCAAGCAC

upper sequence: LOC_Os02g49980.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G41170.1 (Glycine max), 3'ss of exon 5
gtgagttt--actaccttttctgtgtgagcttgtcatccttgagtggctaattactgaa-tgatgtttca--------actgaag---tggtctttctc----atgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTGCAAGGACTCTGTAAACATAGATGTTGTCATTGATTGGCTTATCAAGCAC
|||||||     || |  |  ||| | |  |  |  | ||| |      ||  | ||   |||||| | |        | ||||    |||  ||||||     |  |||||||||| || || |  || || ||| | || || |||||||| ||||| || |||||||| ||||| ||||||||||| |||||||| ||||| ||||| |||
gtgagttctagatatcaatattgtcttatatcttttttctttaaaaaaaaaaaattgtcctgatgtgttatgtaactaattgaacatttggattttctccttggttgatttcagAGGACTTGAGTCAATTAAAGACAGAGAGGTCTGCTGCTATATGATTTCATGCAAGGATTCTGTTAACATAGATGTAGTCATTGACTGGCTAATCAAACAC

upper sequence: LOC_Os02g49980.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G37680.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaagtggtctttctcatgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTGCAAGGACTCTGTAAACATAGATGTTGTCATTGATTGGCTTATCAAGCAC
                      || || || | || |   |||   ||   |   |      ||  |    | |   |     |  | |  | |||||| || ||||   |||  ||| | || |||||||| ||||||||||| || ||||||||  ||||||| ||||  ||||| |||||||| || ||||||
----------------------gtaagtttcttattca-aagtccatacaaaacaatctggattcgagtatatgactttggattgttttgatgcagAGGGCTTGAATCTGTAACAGACAGAGAGGTTTGCTGTTACATGATCTCGTGTAAGGACTCGATAAACATTGATGCGGTCATCGATTGGCTCATTAAGCAC

upper sequence: LOC_Os02g49980.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0006g01090.t01 (Vitis vinifera), 3'ss of exon 6
----------------gtgagtttactaccttttctgtgtgagcttgtcatc--cttgagtggctaa--ttactgaatgatgtttcaactgaagtggtctttctc----------atgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTGCAAGGACTCTGTAAACATAGATGTTGTCATTGATTGGCTTATCAAGCAC
                  |||||| | |     ||  | |     |   ||   | |   |||| ||  ||  |  ||  | | |    |||  |  | ||| ||           ||  ||||||||  ||  | |  || |  |   | || ||  | |||||||||||||| |||||||| || || ||||||||  |||| ||||||||||||||||| |||
gtgagttcagaaccagacgagttttcaataaaatcatttttgatatactatttgcctcgatggcaaacctttttttatattttgtgttttgacatattttttttcctccttggtggtggttttcagAGATCTCAAGTCAATCACAGGTAGAGAGGTGGGTTGCTACATGATCTCGTGCAAGGATTCCGTGAACATAGACCTTGTAATTGATTGGCTTATCAAACAC

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|86512088|gb|CI154721.1|CI154721
EST:     AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACT                         AGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
genomic: AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttac ... tgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
EST: gi|8324374|gb|AU091530.1|AU091530
EST:     AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACT                         AGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
genomic: AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttac ... tgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
EST: gi|88550141|gb|CI480093.1|CI480093
EST:     AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACT                         AGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
genomic: AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttac ... tgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
EST: gi|33808162|gb|CF329970.1|CF329970
EST:     AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACT                         AGGCCTGGAATTGATAAA
genomic: AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttac ... tgtatttcagAGGCCTGGAATTGATAAA
EST: gi|33808160|gb|CF329969.1|CF329969
EST:     AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACT                         AGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
genomic: AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttac ... tgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
EST: gi|33817714|gb|CF334690.1|CF334690
EST:     AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACT                         AGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
genomic: AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttac ... tgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
EST: gi|86600191|gb|CI251561.1|CI251561
EST:     AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACT                         AGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
genomic: AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttac ... tgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
EST: gi|44676654|gb|CR290088.1|CR290088
EST:     AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACT                         AGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
genomic: AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttac ... tgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
EST: gi|86601190|gb|CI251570.1|CI251570
EST:     AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACT                         AGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
genomic: AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttac ... tgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
EST: gi|86834282|gb|CI344042.1|CI344042
EST:     AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACT                         AGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
genomic: AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttac ... tgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
EST: gi|58665641|gb|CK054327.1|CK054327
EST:     AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACT                         AGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
genomic: AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttac ... tgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
EST: gi|88205714|gb|CI205563.1|CI205563
EST:     AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACT                         AGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
genomic: AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttac ... tgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTG
EST: gi|33818441|gb|CF335055.1|CF335055
EST:     AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACT                         AGGCCTGGAATTGATAAAGGGACCGGGAAGTTTGCTGCTACATGATCTCTT
genomic: AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttac ... tgtatttcagAGGCCTGGAATTGATAAAGG-ACCGGGAAGTTTGCTGCTACATGATCTCTT
EST: gi|58586064|gb|CF984372.1|CF984372
EST:     AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACT                         AGGCCTGGAATTGATAAAGGACCGGGAAGTT
genomic: AAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttac ... tgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggctaattactgaatgatgtttcaactgaagtggtctttctcatgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTGCAAGGACTCTGTAAACATAGATGTTGTCATTGATTGGCTTATCAAGCAC
  ggctaat  putative branch site (score: 3)
                                    tctttctcat  putative PPT
     taattact  TA-rich tract