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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