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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatcttaagcctagtcccacaccccagaattaattgagaaaaaaagcttgagtttgccatgggaactaagggttcactcttctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAG

Basic information

species Glycine max
transcript GLYMA17G15990.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G15990.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g50120.2 (Oryza sativa), 3'ss of exon 7
gtatgaatcttaagcctagtcccacaccccagaattaattgagaaaaaaagcttgagtttgccatgggaactaagggttcactcttctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAG
| | || |  |  |     || || |||    |   |||   |      | | ||  | | |||  |  |     ||||   |||| | || | |||| || |||||||||||| |||| |||||||||||||| || |||||||| || || || || ||  || |||| || ||||| |        
gcaggatttctttgttct-tctcaaacc----agccaatcatgctgtgtaacctggatataccagagctaacttcggttatttcttat-tgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTG--------

upper sequence: GLYMA17G15990.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g50120.1 (Oryza sativa), 3'ss of exon 7
gtatgaatcttaagcctagtcccacaccccagaattaattgagaaaaaaagcttgagtttgccatgggaactaagggttcactcttctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAG
| | || |  |  |     || || |||    |   |||   |      | | ||  | | |||  |  |     ||||   |||| | || | |||| || |||||||||||| |||| |||||||||||||| || |||||||| || || || || ||  || |||| || ||||| |||||||||
gcaggatttctttgttct-tctcaaacc----agccaatcatgctgtgtaacctggatataccagagctaacttcggttatttcttat-tgaccagACAGAGCAAATGAGCAGAATTGTTAATGAGCTGGATTCCATTCATTTCTCCATTAAAAAGGCATCACAAATGGTGAAAGAAATTGGTAGGCAG

upper sequence: GLYMA17G15990.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G065105_T02 (Zea mays), 3'ss of exon 7
gtatgaatcttaagcctagtcccaca-----ccccagaattaattgagaaaaaaagcttgagtttgccatgggaactaagggttcactcttctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAG
||| |  ||||   | || | ||| |      ||     || |||  |      |    |        | || || |  ||| |    |||||   || |||| |||||||||||||||||||| |||||| ||||||| ||||||||||| || || || || ||| ||||||| || ||||||||| | |||
gtacgtttctttt-cttatttccagaaggaatccattgctttattatgttgtccaatcaggaaagctaaaggcaattttgggctattccttcttcatc-agACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG

upper sequence: GLYMA17G15990.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G065105_T05 (Zea mays), 3'ss of exon 1
gtatgaatcttaagcctagtcccaca-----ccccagaattaattgagaaaaaaagcttgagtttgccatgggaactaagggttcactcttctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAG-------
||| |  ||||   | || | ||| |      ||     || |||  |      |    |        | || || |  ||| |    |||||   || |||| |||||||||||||||||||| |||||| ||||||| ||||||||||| || || || || ||| ||||||| || ||||||||| | |||       
gtacgtttctttt-cttatttccagaaggaatccattgctttattatgttgtccaatcaggaaagctaaaggcaattttgggctattccttcttcatc-agACAGAACAAATGAGCAGAGTTGTTAATGAGTTGGATTCCATCCATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGGTAAATT

upper sequence: GLYMA17G15990.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G35190.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------gtatgaatcttaagcctagtcccacaccccagaattaattgagaaaaaaagcttgagtttg--ccatgggaacta-----agggttcac-tcttctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAG
                                |  | || |    |||  ||   | | ||   ||     |||        ||| || ||     || ||| ||     |  ||| || | |||  |||  |||| || |||||||| ||||||||||||||||| ||||| || ||||||||  | ||||||||||| ||  ||||||||||||| |||||||||
gtgtgtagttagcccacacttgtttctttccaaacagtcctgcttcta--cctgaatctcatttttttccaagattgtgtatttgtgtgtgaattctgagaattattaagatagtttacattttccttgttcagACCGAGCAAATGAGTAGAGTTGTCAATGAGCTCGATTCTATTCATTTCTCACTCAAGAAAGCCTCCAAGCTGGTCAAGGAAATTGGTAGGCAG

upper sequence: GLYMA17G15990.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv02s0012g00140.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------------------------gtatgaatcttaagcctagtcccacaccccagaattaa---ttgagaaaaaaagcttgagtttgccatgggaactaagg-------gttcactct---tctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAG
                                              |    ||| |  |  | | |  ||   |    | || |   ||       || | ||   |  | ||||| | || | |        || ||| |   | |||||  |||| ||||||||||||||  |||| || ||||| ||||| ||||||||||| || |||||||| ||  |  ||||||||||||| |||||||||
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|58022209|gb|CX708950.1|CX708950
EST:     AAGACACCATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAG                         ACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
genomic: AAGACACCATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAGgtatgaatct ... ctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
EST: gi|58022411|gb|CX709152.1|CX709152
EST:     AAGACACCATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAG                         ACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
genomic: AAGACACCATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAGgtatgaatct ... ctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
EST: gi|193654451|gb|FK596571.1|FK596571
EST:     AAGACACCATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAG                         ACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
genomic: AAGACACCATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAGgtatgaatct ... ctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
EST: gi|192306339|gb|FG996897.1|FG996897
EST:     AAGACACCATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAG                         ACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
genomic: AAGACACCATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAGgtatgaatct ... ctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
EST: gi|151412161|gb|EV281973.1|EV281973
EST:     AAGACACCATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAG                         ACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT
genomic: AAGACACCATAAATGTTGGTACAGATACTGCAGCAGCTCTTAAGGCTCAGgtatgaatct ... ctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaaaaaagcttgagtttgccatgggaactaagggttcactcttctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAG
                                    ttcactcttct  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaatcttaagcctagtcccacaccccagaattaattgagaaaaaaagcttgagtttgccatgggaactaagggttcactcttctatgtctagACGGAACAAATGAGCAGAGTTGTCAATGAGCTGGATTCAATCCATTTCTCTATAAAGAAAGCCTCTAAATTGGTCAAGGAAATCGGTAGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA