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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatcttatgcctagtcccacacctcagaatcaactgagaaaaaaagcttgaatttgccatgtgaactaagggtacactcttctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATGAAGAAAGCCTCTAAATTGGTCAAGGAAATTG

Basic information

species Glycine max
transcript GLYMA05G05720.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G05720.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g50120.2 (Oryza sativa), 3'ss of exon 7
gtatgaatcttatgcctagtcccacacctcagaatcaactgagaaaaaaagcttgaatttgccat-gtgaactaagggtacactcttctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATGAAGAAAGCCTCTAAATTGGTCAAGGAAATTG
| | || |  | ||     || || |||    |  |||    |      | | || || | |||  |  ||||  || ||   |||| | || | ||||||| |||||||| ||| |||| |||||||||||||| || |||||||| || || || || ||  || |||| || |||||||
gcaggatttctttgttct-tctcaaacc----agccaatcatgctgtgtaacctggatataccagagctaacttcggttat-ttcttat-tgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTG

upper sequence: GLYMA05G05720.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g50120.1 (Oryza sativa), 3'ss of exon 7
gtatgaatcttatgcctagtcccacacctcagaatcaactgagaaaaaaagcttgaatttgccat-gtgaactaagggtacactcttctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATGAAGAAAGCCTCTAAATTGGTCAAGGAAATTG--------
| | || |  | ||     || || |||    |  |||    |      | | || || | |||  |  ||||  || ||   |||| | || | ||||||| |||||||| ||| |||| |||||||||||||| || |||||||| || || || || ||  || |||| || |||||||        
gcaggatttctttgttct-tctcaaacc----agccaatcatgctgtgtaacctggatataccagagctaacttcggttat-ttcttat-tgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG

upper sequence: GLYMA05G05720.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G065105_T02 (Zea mays), 3'ss of exon 7
gtatgaatcttatgcctagtcccacacctcagaatcaactgagaaaaaaagcttgaatttgccatgtgaactaagggta---------cactcttctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATGAAGAAAGCCTCTAAATTGGTCAAGGAAATTG--------
||| |  |||| | | || | ||| |     ||||| | ||    |  | | |         || |  | |||| || |          | || |   |    |||||||||||||||| |||||||| |||||| ||||||| ||||||||||| || || || || ||| ||||||| || ||||| |        
gtacgtttctttt-cttatttccagaa---ggaatccattgctttattatgtt--gtccaatcaggaaagctaaaggcaattttgggctattccttcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG

upper sequence: GLYMA05G05720.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G065105_T05 (Zea mays), 3'ss of exon 1
gtatgaatcttatgcctagtcccacacctcagaatcaactgagaaaaaaagcttgaatttgccatgtgaactaagggta---------cactcttctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATGAAGAAAGCCTCTAAATTGGTCAAGGAAATTG---------------
||| |  |||| | | || | ||| |     ||||| | ||    |  | | |         || |  | |||| || |          | || |   |    |||||||||||||||| |||||||| |||||| ||||||| ||||||||||| || || || || ||| ||||||| || ||||| |               
gtacgtttctttt-cttatttccagaa---ggaatccattgctttattatgtt--gtccaatcaggaaagctaaaggcaattttgggctattccttcttcatcagACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGGTAAATT

upper sequence: GLYMA05G05720.2 (Glycine max), 3'ss of exon 4
lower sequence: AT2G35190.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------gtatgaatc-ttatgcctagtcccacacctcagaatcaactgagaaaaaaagcttgaatttgccatgtga-----actaagg--gtacac-tcttctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATGAAGAAAGCCTCTAAATTGGTCAAGGAAATTG--------
                            |   ||   |  ||| |   ||   | ||||   |   |  |||        |||  | ||   | |||     | ||||   ||  || | |||  |||  |||| || |||||||||||||||||||||||||| ||||| || ||||||||  | ||||||||||| ||  |||||||||||||||        
gtgtgtagttagcccacacttgtttctttccaaacagtcctgcttctacctgaatctcatttttttccaagattgtgtatttgtgtgtgaattctgagaattattaagatagtttacattttccttgttcagACCGAGCAAATGAGTAGAGTTGTCAATGAGCTCGATTCTATTCATTTCTCACTCAAGAAAGCCTCCAAGCTGGTCAAGGAAATTGGTAGGCAG

upper sequence: GLYMA05G05720.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0012g00140.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------------------------------gtatgaatcttatgcctagt-cccacacctcagaatcaactgagaaaaaaagcttga-atttgccatgtgaactaag--ggtacactct---tctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATGAAGAAAGCCTCTAAATTGGTCAAGGAAATTG--------
                                                     | |  ||   ||    ||  |    |  | |   |    |  |||      | | | |  ||  |  | || |       |  ||| |   | |||||  |||| ||||||||||| ||  |||| || ||||| ||||| ||||||||||| || |||||||| ||  |  |||||||||||||||        
gtctgtacctcatcaatattaaatttttttctgattctgacacattgctacaatttagattcaatttacagcacttgtattttacctttctttttgaaggttttcctaagacatggtagcttaagtgtttcaatttactttacgtttatgttcagACTGAACAAATGAGCAGGATTGTTAACGAGCTAGATTCTATCCATTTCTCAATCAAGAAAGCTTCACAGCTGGTCAAGGAAATTGGTAGGCAG

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|192301656|gb|FG994378.1|FG994378
EST:     AAGACACAATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAG                         ACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
genomic: AAGACACAATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAGgtatgaatct ... ctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
EST: gi|5509749|gb|AI856307.1|AI856307
EST:     TGACAC-NTNANATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAG                         ACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
genomic: AGACACAAT-AAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAGgtatgaatct ... ctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
EST: gi|58018223|gb|CX704965.1|CX704965
EST:     AAGACACAATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAG                         ACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
genomic: AAGACACAATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAGgtatgaatct ... ctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
EST: gi|57575682|gb|CX548657.1|CX548657
EST:     AAGACACAATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCT---                         -CAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
genomic: AAGACACAATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAGgtatgaatct ... ctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
EST: gi|16344307|gb|BI969902.1|BI969902
EST:     AAGANNNAATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAG                         ACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
genomic: AAGACACAATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAGgtatgaatct ... ctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaaaaaagcttgaatttgccatgtgaactaagggtacactcttctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATGAAGAAAGCCTCTAAATTGGTCAAGGAAATTG
                                      cactcttct  CT-rich tract
           ttgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaatcttatgcctagtcccacacctcagaatcaactgagaaaaaaagcttgaatttgccatgtgaactaagggtacactcttctatgtctagACAGAACAAATGAGTAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATGAAGAAAGCCTCTAAATTGGTCAAGGAAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA