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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTAGTCCTTGGCAACAAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaagtggtctttctcatgtatttcag

Basic information

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

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g49980.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G089454_T03 (Zea mays), 5'ss of exon 4
TGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTAGTCCTTGGCAACAAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaagtggtctt---tctcatgtatttcag
||||||||||||| ||||||||||||||||| || || |||||||||||||||||||||||||||||||   |||| ||||| || ||||||||||||||||||| | | | | |  | ||  |  ||     ||| ||      ||| || ||| || ||  |||| ||||||   | ||   | |  ||| ||||||
TGCTGACAAAACAGTCTTTAGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaat-cttcatttgcctacgc-----atcatt------ctactttctgcattataattcagctgaagctcttttgacttttttgt-tttcag

upper sequence: LOC_Os02g49980.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G171060_T02 (Zea mays), 5'ss of exon 6
TGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTAGTCCTTGGCAACAAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaagtggtct-ttctcatgtatttcag-------
||||||| ||||| ||||| ||||||||||| || || ||||||||||||||||||||||||||||||||  |||| ||||| || |||||||||||||||| || | |  |||||   | ||    ||  | ||  |         | || ||| ||||| | ||| || |||   |||  |||| |   |||  |       
TGCTGACGAAACAGTCTTTGGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctca--accttcatt-tgcttactcataattat---------actttctgcatgatatctcagctcaagctctctgctctcttccctttttgttttcag

upper sequence: LOC_Os02g49980.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA14G39540.1 (Glycine max), 5'ss of exon 5
TGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTAGTCCTTGGCAACAAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagttt--actaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaac-tgaagtggtctttctcatgt---atttcag
|  |||||||||  |||||   |||||||||||| || || ||||| |||||||||||||||||||||||| |||| |||||||| ||||| ||||| |||||||||      | |  |  ||  | |  |  || || ||       | |||| ||||   ||| |  |       || | ||   | ||    |||||||
TATTGACAAAACCTTCTTTGAGTGGGATTCCTTTGCTTGTTCTTGGAAACAAAATTGACAAGTCAGAAGCTCTTTCTAAGCAAGCATTGGTAGATCAGCTgtgagttctagaaatcaatattgccttatatcatcttcttttt----tttattattgaaatttgtcttgatgctttatgattttctccttgggtgatttcag

upper sequence: LOC_Os02g49980.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G41170.1 (Glycine max), 5'ss of exon 5
TGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTAGTCCTTGGCAACAAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagttt--actaccttttctgtgtgagcttgtcatccttgagtggctaattactgaa-tgatgtttca--------actgaag---tggtctttctc----atgtatttcag
|  |||||||||  |||||   || ||||||||| || || ||||| |||||||||||||||||||||||| |||| |||||||| ||||| ||||| |||||||||     || |  |  ||| | |  |  |  | ||| |      ||  | ||   |||||| | |        | ||||    |||  ||||||     |  |||||||
TATTGACAAAACCTTCTTTGAGTGCGATTCCTTTGCTTGTTCTTGGAAACAAAATTGACAAGTCAGAAGCTCTTTCTAAGCAAGCATTGGTAGATCAGCTgtgagttctagatatcaatattgtcttatatcttttttctttaaaaaaaaaaaattgtcctgatgtgttatgtaactaattgaacatttggattttctccttggttgatttcag

upper sequence: LOC_Os02g49980.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G37680.1 (Arabidopsis thaliana), 5'ss of exon 4
TGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTAGTCCTTGGCAACAAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttactaccttt--tctgtgtgagcttgtc-atccttgagtggctaattactgaatgatgtttcaactgaagtggtctttctcatgtatttcag
|||| || ||||  ||||||  ||| |||||| | ||  | |||||||||||||| || ||||| |||||| | || |||||||| |||||||||||||||| |||||  ||       ||  |   |     ||     | ||||   | | |  || ||  |||||  | || ||                      
TGCTAACGAAACCGTCTTTAAATGGCATTCCTCTTCTGATTCTTGGCAACAAAATCGATAAGTCTGAAGCTCTCTCTAAGCAAGCTTTGGTTGATCAACTgtaagtttcttattcaaagtccatacaaaacaatctggattcgagtatatgact-ttggat--tgttttga-tgcag----------------------

upper sequence: LOC_Os02g49980.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv14s0006g01090.t01 (Vitis vinifera), 5'ss of exon 6
TGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTAGTCCTTGGCAACAAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttactaccttttctgtgtgagcttg--tcatccttgagtggctaattac-tgaatgatgtttcaactgaagtggtct---ttctcatgtatttcag------------------------
|  ||||||||| ||| ||  |||| ||||||||||| ||  |||||||||||||||||| ||| |||||| ||||  ||||| ||||||| | ||||||||||||| |  |||      || |    |    ||||  ||||    ||| || | |  |||      |   |    |  | |   || | |  |||||                           
TCTTGACAAAACCATCCTTGACTGGAATTCCTTTACTTGTTGTTGGCAACAAAATTGACAGGTCGGAAGCTCTTTCGGAGCAATCGTTGGTGGGTCAACTgtgagttcagaaccagacgagttttcaataaaatcatttttgatatactatttgcctcgatggcaaacctttttttatattttgtgttttgacatattttttttcctccttggtggtggttttcag

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

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTAGTCCTTGGCAACAAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaagtggtctttctcatgtatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG