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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaataagcttttgtttatacttgttttttttttatcatgatggcctacatttttcacaacagtaataagctttggagatctctactaaatttcac...

Basic information

species Oryza sativa
transcript LOC_Os05g49200.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM5G899123_T01 (Zea mays), 5'ss of exon 3
GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaataagcttttgtttatacttgttttttttttatcatgatg-gcctacatttttcacaacagtaataagctttggagatctctactaaatttcac
| ||||||||  |||| ||| |||| || ||||| |||||||| || ||||||||||||||||||||| ||  | |||| | |||| ||   |  |||    |   |  ||| || ||  |||||     |  |  | |  |||   |      |  |||  |   
GGTTTTGTGCCGGCGGCTGTGCAGCCATGGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAgtaagttttgagctct-gtttttatcggcatttgagattgaagcatgtgcttagtttttttgtgtctttggtgatattttacgtatataataaaacctttt

upper sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G370357_T01 (Zea mays), 5'ss of exon 6
GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaataagcttttgtttatacttgttttttttttatcatgatg-gcctacatttttcacaacagtaataagctttggagatctctactaaatttcac
| ||||||||  |||| ||| ||||||| ||||| |||||||| || ||||||||||||||||||||| ||  | |||| | |||| ||   |  |||    |   |  ||| || ||  | |||     |  |  | |  |||   |      |  |||  |   
GGTTTTGTGCCGGCGGCTGTGCAGCTATGGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAgtaagttttgagctct-gtttttatcggcatttgagattgaagcatgtgcttagttgttttgtgtctttggtgatattttacgtatataataaaacctttt

upper sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G035636_T01 (Zea mays), 5'ss of exon 8
GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaataagcttttgtttatacttgtttttttt-ttatcatgatggccta--catttttcacaacagtaataagctttggagatctctactaaatttcac
| ||||||||  |||| ||| |||| || ||||| |||||||| || |||||||||||||||||| || ||  | |||| |   || ||   |  |||    ||         || ||    |||||     |  |  | |  |||  |  | | || ||||      
GGTTTTGTGCCGGCGGCTGTGCAGCCATCGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAataagttttgagctctgtattttatcggcatttgagattgaagcaggtgcttagtttttttttgtgtctttggtgatatttt-acgtatataataaaacct--

upper sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G065757_T02 (Zea mays), 5'ss of exon 8
GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaataagcttttgtttatacttgttttttttttatcatgatggcc-tacatttttcacaacagtaataagctttggagatctctactaaatttcac
| ||||||||  | || ||| |||| || ||||| |||||||| || ||||||||||||||||||||| ||  | |||| |   || |   | |   |||   ||       ||     | ||||     |  |  | |  |||   |      |  |||  |   
GGTTTTGTGCCGGTGGCTGTGCAGCCATCGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAgtaagttttgagctctgtgttttttatctgcatttgagattgaagcagctgcttagtttttgtgtctatggtgatattttacgtatataatgaaaccttt-

upper sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G057724_T01 (Zea mays), 5'ss of exon 11
GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaataagcttttgtttatacttgtttttttt-ttatcatgatggcctacatttttcacaacagtaataagctttggagatctctactaaatttcac
| ||||||||  |||| ||| ||||| | ||||| |||||||| || ||||||||||||||||||||| ||  | |||| | |||| ||   |  |||    ||         || ||  |||||     |  |  | |  |||   |     ||  |||  |   
GGTTTTGTGCCGGCGGCTGTGCAGCTGTCGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAgtaagttttgagctct-gtttttatcggcatttgagattgaagcaggtgcttagtttttttgtgtctttggtgatattttacgtatattataaaacctttt

upper sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G153977_T01 (Zea mays), 5'ss of exon 2
GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaataagcttt-tgtt-tatacttgttttttttttatca--tgatggcctacatt-tttcacaacagtaataagctttggagatctctactaaatttcac
| ||||||||| | |||||| |||| |||||||| |||||||| || ||||||||||||||||||||| ||  | |||||| |||| | ||  ||        | ||    |  |||  | ||   |||  | |  | ||  ||||| | || | | |  |   ||    
GGTTTTGTGCTGGTGGTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAgtaagttttgagctttgtgttctttatctgcagaacaatgatgggttattgggattcaccattttgcgattg-aagcagcttcgtagtttttttttctgtt----

upper sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G001713_T01 (Zea mays), 5'ss of exon 4
GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaataagcttttgtttatacttgtttttttt-ttatcatgatggccta--catttttcacaacagtaataagctttggagatctctactaaatttcac
| ||||||||  |||| ||| |||| || ||||| |||||||| || |||||||||||||||| |||| ||  | |||| |  ||| ||   |  |||    ||         || ||    |||||     |  |  | |  |||  |  | | || ||||      
GGTTTTGTGCCGGCGGCTGTGCAGCCATCGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCATAgtaagttttgagctctgttttttatcggcatttgagattgaagcaggtgcttagtttttttttgtgtctttggtgatatttt-acgtatataataaaacct--

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|33795396|gb|CF323568.1|CF323568
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|29687282|gb|CB683557.1|CB683557
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|58668482|gb|CK057168.1|CK057168
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|33683538|gb|CF311777.1|CF311777
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|58596651|gb|CK007179.1|CK007179
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|125863426|gb|EL586708.1|EL586708
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|29675128|gb|CB671403.1|CB671403
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|117249803|gb|CT863399.1|CT863399
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|29637768|gb|CB642777.1|CB642777
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGACAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|58668099|gb|CK056785.1|CK056785
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|29660989|gb|CB657264.1|CB657264
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|29627821|gb|CB632832.1|CB632832
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAA
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAA
EST: gi|58587529|gb|CF985837.1|CF985837
EST:     AGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCGATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: AGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|55827430|gb|AU030192.2|AU030192
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|218480608|gb|FG959514.1|FG959514
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|218495569|gb|FG950148.1|FG950148
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|88396547|gb|CI601030.1|CI601030
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|86847366|gb|CI286963.1|CI286963
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTA
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTA
EST: gi|58592991|gb|CF991299.1|CF991299
EST:     AGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCGATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: AGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|33381232|gb|CF196575.1|CF196575
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|58599924|gb|CK010452.1|CK010452
EST:     TTGTTCAGCTATNAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: TTGTTCAGCTAT-AGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|218481767|gb|FG945139.1|FG945139
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|218486960|gb|FG945468.1|FG945468
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
EST: gi|218484121|gb|FG947440.1|FG947440
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGG
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGG
EST: gi|29639939|gb|CB644948.1|CB644948
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         GCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACT
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACT
EST: gi|66924030|gb|CX110878.1|CX110878
EST:     GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACA                         ACCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC
genomic: GTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaata ... atcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTTGTGCTAGCGGTTGTTCAGCTATAGCAGACTCTGGAACATCATTGCTTGCTGGCCCCACAgtacgtaataagcttttgtttatacttgttttttttttatcatgatggcctacatttttcacaacagtaataagctttggagatctctactaaatttcac

- - - - - - - - - - TCAGCT