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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctcatagtccgttttatggtttaaattgcatatcccatatagtatagtattggtcatgcatacatctgttattgtccttaacaatatgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCAACACTGCTCGTGACGCCATTCAGTACTCCAT

Basic information

species Oryza sativa
transcript LOC_Os04g59040.2
intron # 6
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 7
gtatcctca---tagtccgttttatggtttaa-attgcatatcccata-------tagtatagtattggtcatgcatacatctgttattgtccttaacaatatgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCAACACTGCTCGTGACGCCATTCAGTACTCCAT
||||||||    || | | |||  || |||   | | || || |  ||       | | ||  |     ||| |||   |    |     |||||| | ||||  | | ||||||||| || |||||||| || || || ||||||||||||||||| || |  || ||||  || |||||||||||||||||
gtatcctccgcttaattcatttgctgttttcttactacacatgctctagcatattttggatgatcacattcacgcaggtaggcatatgcttccttagcgatat-ctctcagACAAGAAAAACGAGAACAAAGAAGTCGCAGTTGATGCATTCTTGCCCGCGACAACAGCTCAAGAAGCCATTCAGTACTCCAT

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 7
gtatcctcatagtccgttttatggttta--aattgcatatcccatatagtatagt---attggtcatgcatacatctgttattgtccttaacaatatgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCAACACTGCTCGTGACGCCATTCAGTACTCCAT------------------
|||||||  | |     | ||| ||||    | | || |   | | ||||||| |      | |||     |||  | | |   |||||| |  |||  || |||| |||||||||||||| || ||||||||||| ||||||||||||||||| | ||| ||||| || |||||||||||||||||                  
gtatcctgctcgattcatctattgttttctgactacacaatgc-tctagtatatttgggacgatcacatccacaggtttaagcttccttagcggtat-cttctagATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGACCACAGCTCGAGAGGCCATTCAGTACTCCATGTAAGCTCAGCTTGACAC

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G061928_T02 (Zea mays), 3'ss of exon 7
gtatcctcatagtccgttttatggttta--aattgcatatcccatatagtatagt---attggtcatgcatacatctgttattgtccttaacaatatgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCAACACTGCTCGTGACGCCATTCAGTACTCCAT
|||||||  | |     | ||| ||||    | | || |   | | ||||||| |      | |||     |||  | | |   |||||| |  |||  || |||| |||||||||||||| || ||||||||||| ||||||||||||||||| | ||| ||||| || |||||||||||||||||
gtatcctgctcgattcatctattgttttctgactacacaatgc-tctagtatatttgggacgatcacatccacaggtttaagcttccttagcggtat-cttctagATAAGAAGAATGAGAATAAAGAGGTTGCTGTCGATGCATTCTTGCCTGCGACCACAGCTCGAGAGGCCATTCAGTACTCCAT

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 7
---------------gtatcctcatagtccgttttatggtttaaattgcatatcccatatagtatagtattggtcatgcatacatctgttattgtccttaacaatatgttt-ttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCAACACTGCTCGTGACGCCATTCAGTACTCCAT
                ||| |  |||    | |  |||  ||   ||     | |   |||||||  |  |    |   ||| |    | | ||   ||   ||||| ||  | ||||||||||||||||||||||||||| || ||| |||  ||  | |||||   ||||||   |||  |||| |||||||| ||
gtatccttaaaaatcttattccaataacttgatacatgagtttctttaagattacttcatagtattttcataaa-aaaaataaaaaattgagtgcatttcttaatatattgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCCGTTGAATCCATCCAGTACTCAAT

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 5
gtatcctcatagtccgtttt---atggtttaaat---tgcatatcccatatagt------atagtattggtcatgcatacatctg-ttattgtccttaacaatatgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCAACACTGCTCGTGACGCCATTCAGTACTCCAT
||||||| | |   | | ||   ||   ||  ||   |   | | |  ||   |      ||||||||  ||||  | | |  || ||    | ||||||| ||| |  | ||||||||||||||||||||||||||| || ||| |||  ||  | |||||   |||||||  |||  |||| |||||||| ||
gtatccttaaaaatcttattccaataactttgatacctaagttttctttaagattactttatagtattt-tcataaaaaaaattgattgcatttcttaaca-tatttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCTGTTGAATCCATCCAGTACTCAAT

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatcctcatagtccgttttatggtttaaattgcatatcccatatagtatagtattggtcatgcatacatctgttattgtccttaacaatatgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCAACACTGCTCGTGACGCCATTCAGTACTCCAT
||||||| | |  |  |||||    || | | | |          |  | |            |||   | | ||  | || ||||| | |   |   |||||||||||||||||||||||| ||||| ||  |||  ||  | |   |     |||||  ||| |||||||||||||| ||
gtatccttaaaacctattttaatacttgattagga----------aacaaaac----------catttcttttttgctatctttaaccaaaatataacagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT

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|58669944|gb|CK058630.1|CK058630
EST:     GTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTGGCCTGCCA
genomic: GTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88266037|gb|CI376939.1|CI376939
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|86873424|gb|CI341649.1|CI341649
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|33684219|gb|CF312458.1|CF312458
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|86527296|gb|CI167502.1|CI167502
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88320691|gb|CI525633.1|CI525633
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|86834579|gb|CI340696.1|CI340696
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|86846050|gb|CI347237.1|CI347237
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88384252|gb|CI551178.1|CI551178
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|33684220|gb|CF312459.1|CF312459
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGGAGGTTGCTGTTGATGCATTCTTGCCTGCC
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGG-AGGTTGCTGTTGATGCATTCTTGCCTGCC
EST: gi|89171018|gb|CI040295.1|CI040295
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88450730|gb|CI549816.1|CI549816
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88291938|gb|CI532530.1|CI532530
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88963306|gb|CI028322.1|CI028322
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88441295|gb|CI538738.1|CI538738
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88555507|gb|CI485770.1|CI485770
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGAGT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|88965200|gb|CI009236.1|CI009236
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|86498205|gb|CI140838.1|CI140838
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
EST: gi|55434347|gb|CV730295.1|CV730295
EST:     TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA
genomic: TGAGCTGTCTCCTCACCGCCTCCAAGAGATTAAACGCTTCTTTGAAGACTgtatcctcat ... atgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatagtattggtcatgcatacatctgttattgtccttaacaatatgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCAACACTGCTCGTGACGCCATTCAGTACTCCAT
 gtccttaac  putative branch site 
                                              tgttttt  putative PPT
                                     ttaacaatatgttttt  TA-rich tract