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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaatacttccatttttcagtttgatttatcatgctgaaaagttatggtaatgttatgaactactggcatcttatatttttacttttttag

Basic information

species Glycine max
transcript GLYMA07G34680.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G34680.2 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os06g43140.1 (Oryza sativa), 5'ss of exon 5
GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaatacttccatttttcagtttgatttatcatgctgaaaagttatggtaatgttat-gaactactggcatcttatatttttacttttttag
||||||| ||||||||||| ||||||||||| ||||||||||||||| | || ||||  |   | || || |||  |           |   ||  | || || | ||   ||     || || | | | | | | |||| | |   | ||
GGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGACgtatg---tgctcccttttccc-----------ttgcgcccataatttgttgttgcgtccccaaaatatttgtaacatct-ttttcattgcatcag

upper sequence: GLYMA07G34680.2 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os02g09460.1 (Oryza sativa), 5'ss of exon 5
GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgag-------caatacttccatttttcagtttgatttatcatgctgaaaagttatggtaatgttatgaactactggcatcttatatttttacttttttag
| || |||||||||||||| |||||||||||||| |||||||||||| | || ||||  |        ||| | | |||| ||         | |   | ||   |||| | |  ||    ||     | | |  |||| | |||  | |  || ||
GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttccctaatccctacattcttttccccatgtcaattttctcccaagtga-gccaacaaaatattaaattagattcttct-tttgcattgcttcag

upper sequence: GLYMA07G34680.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G141241_T03 (Zea mays), 5'ss of exon 3
GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaa--tacttccatttttcagtttgatttatcatgctgaaaagttatggtaatgttatgaactactggcatcttatatttttacttttttag
| || |||||||||||||| ||||| |||||||| |||||||||||| | || | ||  | |   | ||| |||  ||    || | || | |||     |||||||  | ||   |     | ||     || ||                
GACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGATgtatgtagactcctttcatcctttccattaacttttgatgtgtccaagttatatttataacacttggt-ctattgcctcat----------------

upper sequence: GLYMA07G34680.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G092988_T01 (Zea mays), 5'ss of exon 4
GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaatacttccatttttcagtttgatttatcatgctgaaaagttatggtaatgt-tatgaactactggcatcttatatttttacttttttag
| || |||||||||||||| ||||||||||| || |||||||||||| | || ||||  |  ||  |  || || | | ||        |||  ||  |  || |  || ||| ||  |  |  |  ||  ||  || ||    | |  ||
GACCTGATGACATGCCAGCACATATTAAATCTTCTATGTTTGGTTGTTCCCTAACgtacgtgat-ttctcacttcttatttcttccctccattatgtta--ttcttctactgtgtagaagtttttaacagtttgcatcttgctctatgcag

upper sequence: GLYMA07G34680.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM5G890647_T02 (Zea mays), 5'ss of exon 3
GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaa--tacttccatttttcagtttgatttatcatgctgaaaagttatggtaatgttatgaactactggcatcttatatttttacttttttag
| || |||||||||||||| ||||| |||||||| |||||||||||| | || | ||  | |   | ||| |||  ||    || | || | |||     |||||||  | ||   |     | ||     || |                 
GACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGATgtatgtagactcctttcatcctttccattaacttttgatgtgtccaagttatatttataacacttggt-ctattgcctcag----------------

upper sequence: GLYMA07G34680.2 (Glycine max), 5'ss of exon 5
lower sequence: AT1G21065.1 (Arabidopsis thaliana), 5'ss of exon 5
GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaatacttccatttttcagtttgatttatcatgctgaaaagttatggtaatgttatgaactactggcatcttatatttttacttttttag------
| || |||||||||||||||||||| || ||||| |||||||| |||  |||||||||||| | | |   ||| |  |   |  |||  |||    | || ||||  ||   ||  ||  | |    | |   | ||| | | ||||         
GTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCACgtgagctacaatcatattata-accgtagtttgacatagc-acaatttattttagcttttggatgttcacttaacaagtgtttgttcattttggtctgcag

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|209715443|gb|BW684715.1|BW684715
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|18692788|gb|BM521636.1|BM521636
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|31456074|gb|CD398102.1|CD398102
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|9984433|gb|BE658541.1|BE658541
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|31474712|gb|CD416740.1|CD416740
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|15663182|gb|BI700553.1|BI700553
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|23733010|gb|BU764686.1|BU764686
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|16347696|gb|BI973291.1|BI973291
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|7692412|gb|AW760519.1|AW760519
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|209715444|gb|BW684716.1|BW684716
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|31472535|gb|CD414563.1|CD414563
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|298175025|gb|HO018020.1|HO018020
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|23733507|gb|BU764952.1|BU764952
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|120496558|gb|EH224725.1|EH224725
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|298172343|gb|HO019383.1|HO019383
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|10238632|gb|BE807520.1|BE807520
EST:     AATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: AATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|6135090|gb|AW133483.1|AW133483
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGGTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|120496987|gb|EH225154.1|EH225154
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
EST: gi|27425952|gb|CA937472.1|CA937472
EST:     GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC                         GATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG
genomic: GATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaata ... acttttttagGATACCGATTACAAATGGCAAGCTTAACATGGGGACATGGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaatacttccatttttcagtttgatttatcatgctgaaaagttatggtaatgttatgaactactggcatcttatatttttacttttttag

- - - - - - -  CAGCTC
- - - - - - - - AGCTCA