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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttaatgtacatacatgaaagttaaactcttaattttaattgtccacatcattcaaattatgttttgtctgacttggtctagttcttgatcattatagTGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGGCCTTTCAGATGATGACATTTTCCGCGGAAGAGTTACAGACAAATGGCGG

Basic information

species Glycine max
transcript GLYMA14G03500.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G03500.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0028g00960.t01 (Vitis vinifera), 3'ss of exon 4
tctttaatgtacatacatgaaagttaaactcttaattttaattgtccacatcattcaaattatgttttgtctgacttg-gtctagttcttgatcattatagTGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGGCCTTTCAGATGATGACATTTTCCGCGGAAGAGTTACAGACAAATGGCGG
|  | |    ||  ||||| | | |  | | |   |  |   ||| |  |       |||| |    | |  ||||   ||||  |  || || ||   |||||||| || |||||| ||||||||||||| |||||  | | || ||| ||||| ||||||||||||||  |||| || | ||| || ||||| ||| ||
tgataagaaaaccaacatggatgattgattttctgtcctttgtgttctaaaagcctgaattcttcggt-ttggactcatgtcttttgtttaattatatcagTGCTAGGAGGGGAAGAATATATCTCCCACAGGATGAGCTTGAACGAGCAGGCCTGTCAGATGATGACATACTCCGTGGGAAAGTGACTGACAAGTGGAGG
















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|7235172|gb|AW570502.1|AW570502
EST:     CTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGA                         TGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGG
genomic: CTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGAgtaaggttct ... atcattatagTGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGG
EST: gi|192318814|gb|FK011428.1|FK011428
EST:     CTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGA                         CGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCGCAAGCTGG
genomic: CTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGAgtaaggttct ... atcattatagTGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGG
EST: gi|192314403|gb|FK008401.1|FK008401
EST:     CTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGA                         CGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCGCAAGCTGG
genomic: CTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGAgtaaggttct ... atcattatagTGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGG
EST: gi|192314402|gb|FK008400.1|FK008400
EST:     CTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGA                         CGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCGCAAGCTGG
genomic: CTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGAgtaaggttct ... atcattatagTGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGG
EST: gi|9204530|gb|BE330754.1|BE330754
EST:     CTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGA                         TGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGG
genomic: CTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGAgtaaggttct ... atcattatagTGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGG
EST: gi|51341598|gb|CO982915.1|CO982915
EST:     CTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGA                         TGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGG
genomic: CTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGAgtaaggttct ... atcattatagTGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGG
EST: gi|9205460|gb|BE331684.1|BE331684
EST:     CTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGA                         TGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGG
genomic: CTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGAgtaaggttct ... atcattatagTGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacatcattcaaattatgttttgtctgacttggtctagttcttgatcattatagTGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGGCCTTTCAGATGATGACATTTTCCGCGGAAGAGTTACAGACAAATGGCGG
       attcaaattatgtttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttaatgtacatacatgaaagttaaactcttaattttaattgtccacatcattcaaattatgttttgtctgacttggtctagttcttgatcattatagTGCTAGAAGAGGAAGAGTATATCTCCCACAAGATGAATTGGCACAAGCTGGCCTTTCAGATGATGACATTTTCCGCGGAAGAGTTACAGACAAATGGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - -catacat
- - - - - - - - - - - - - - - - - - - - - - -ccacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttcttg