Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcactattttgccaatttctcccttatatttttgttcatgaaatttctactggttgatagaatatagacgctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAAGACCAGCTTGAAGAAAGAATGGCACGCATCAAAGAGGATCCATCTCTGA

Basic information

species Glycine max
transcript GLYMA06G47830.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G47830.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g04270.t01 (Vitis vinifera), 3'ss of exon 4
---------------gtcactattttgccaatttctcccttatatttttgttcatga------aatttctactggttgatagaatatagacgctgtaa-----cagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAAGACCAGCTTGAAGAAAGAATGGCACGCATCAAAGAGGATCCATCTCTGA
                    | |||   | ||||||   ||||  |||| |  ||||      ||| ||   |    |||  ||| |    |   ||      |||||||| ||||||||   ||||||||| | |||  |||||||| || | || ||||||||||||||||||||||||||||| ||||| ||||||||  |||
gtttgtatggtctttcatgttgtttaagctatttctgtgttattattttatgtatgataaaataatatcatttttcagattaaatttcagtggcatattttttcagGATCCATCTATGTCCAGCATGCTTGAGAATTTGGCTAATCCAACACACAAGGACCAGCTTGAAGAAAGAATGGCACGCATTAAAGAAGATCCATCATTGA
















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|192309988|gb|FK002512.1|FK002512
EST:     ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAG                         GATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
genomic: ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAGgtcactattt ... gctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
EST: gi|209715174|gb|BW665651.1|BW665651
EST:     ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAG                         GATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
genomic: ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAGgtcactattt ... gctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
EST: gi|10843162|gb|BF066475.1|BF066475
EST:     ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAG                         GATCCGTCTATGTCTGCCATGCTTGAAAGTTNTTCTAATCCATCAAATAAA
genomic: ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAGgtcactattt ... gctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
EST: gi|254335741|gb|GR847269.1|GR847269
EST:     ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAG                         GATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
genomic: ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAGgtcactattt ... gctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
EST: gi|17152886|gb|BM142819.1|BM142819
EST:     ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAG                         GATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
genomic: ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAGgtcactattt ... gctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
EST: gi|10710560|gb|BF010278.1|BF010278
EST:     ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAG                         GATCCGTCTATGTCTGCCATGCT
genomic: ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAGgtcactattt ... gctgtaacagGATCCGTCTATGTCTGCCATGCT
EST: gi|193386235|gb|FK349441.1|FK349441
EST:     CATGGCTGAGCGCCTGGGTAATGCATTGATGCAG                         GATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
genomic: CATGGCTGAGCGCCTGGGTAATGCATTGATGCAGgtcactattt ... gctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
EST: gi|10709138|gb|BF008862.1|BF008862
EST:     ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAG                         GATCCGTCTATGTCTGGCATGGCTTGAA-GTTTTTCTAATCCCATCNA-TA
genomic: ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAGgtcactattt ... gctgtaacagGATCCGTCTATGTCTGCCATG-CTTGAAAGTTTTTCTAATCC-ATCAAATA
EST: gi|254335876|gb|GR847404.1|GR847404
EST:     ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAG                         GATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
genomic: ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAGgtcactattt ... gctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
EST: gi|193492232|gb|FK455258.1|FK455258
EST:     ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAG                         GATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
genomic: ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAGgtcactattt ... gctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
EST: gi|4297313|gb|AI442600.1|AI442600
EST:     ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAA                         GATCCGTCTATGTCTGCCATGCTTGAAAGTTATTCTAATCCATCAAATAAA
genomic: ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAGgtcactattt ... gctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
EST: gi|21601758|gb|BQ612089.1|BQ612089
EST:     ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAG                         GATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
genomic: ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAGgtcactattt ... gctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
EST: gi|5605985|gb|AI900083.1|AI900083
EST:     ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAG                         GATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
genomic: ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAGgtcactattt ... gctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
EST: gi|151407493|gb|EV277308.1|EV277308
EST:     ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAG                         GATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA
genomic: ATCCTAATTTTATGACCATGGCTGAGCGCCTGGGTAATGCATTGATGCAGgtcactattt ... gctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatttttgttcatgaaatttctactggttgatagaatatagacgctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAAGACCAGCTTGAAGAAAGAATGGCACGCATCAAAGAGGATCCATCTCTGA
                           ggttgat  putative branch site (score: 5)
                                atagaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcactattttgccaatttctcccttatatttttgttcatgaaatttctactggttgatagaatatagacgctgtaacagGATCCGTCTATGTCTGCCATGCTTGAAAGTTTTTCTAATCCATCAAATAAAGACCAGCTTGAAGAAAGAATGGCACGCATCAAAGAGGATCCATCTCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT