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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCATCACATGCTGTATCCTATGACAGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctctcagatttctccctttctcttctttccatccctattaacatttttgtgttcctagactttaactaggtagcttgaggttatatttttgt...

Basic information

species Glycine max
transcript GLYMA20G30820.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30820.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os05g36120.1 (Oryza sativa), 5'ss of exon 6
GTTCATCACATGCTGTATCCTATGACAGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctctcagatttctccctttctcttctttccatccctattaacatttttgtgttcctagactttaactaggtagcttgaggttatatttttgt-
 |||| |||||| |||||||||| || ||||| || ||  ||||||| ||     |  |||||| |||||| |||||||| |||||||||||||||||||||||||||| | ||  | |||| |  ||    |   |   |    || | ||   ||| | | |||    |   |  | |     ||| |   || |    
ATTCACCACATGATGTATCCTATAACTGTGGAGGTTCTACATCAAGTTTTCAAAGCTTATGGATATGTGGAGAAGATTGTCACATTTCAGAAGTCAGCTGgtcagattcccccatctctctctcactccgcacacacatgcatagttgatatggatgt-tacttagcagatgcatgtgaatggcaaggctgatttatcaat

upper sequence: GLYMA20G30820.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os01g64770.2 (Oryza sativa), 5'ss of exon 6
GTTCATCACATGCTGTATCCTATGACAGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctctcagatttctccctttctcttctttccatc-cctattaacatttttgtgttcctagactttaactaggtagcttgaggt-tatatttttgt-
 ||||||| ||||| || ||||| ||  | || |||||  ||||||| ||||||||| |||||| |||||| ||||| || |||||||| |||||||| ||||||||||| ||  |  ||||  | || ||   |||   |   || |    | |||   || | |||    |   || |    |||||  ||| |  | || 
ATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGGAGAAGATAGTCACATTTCAAAAGTCAGCCGgtcagattctttct-acctctcattctcactctattcttgcatttaatgcagtgttttccttgccagatagcatgcagatta--tgaggcgtatttcatagtt

upper sequence: GLYMA20G30820.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G070113_T01 (Zea mays), 5'ss of exon 6
GTTCATCACATGCTGTATCCTATGACAGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctctcagatttctccctttctcttctttc-catccctattaacatttttgtgttcctagactttaactaggtagcttg-aggttatatttttgt-
 | || |||||| | |||||||| || ||||| || ||  ||||||||||     |  |||||| |||||| |||||||| |||||||| |||||||||||| ||||| ||   | | |||  || | ||  |   | ||     |   |  | |   | |||  |  |  | || |||| || ||    |  ||   | |  
ATCCACCACATGATCTATCCTATAACGGTGGAGGTTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagattttcct-gctctctttctctttcaccacgcacacgtgcaccta-gtatgcattttctgattcccttac-aggttgcatgtgaatggtaaggtggat

upper sequence: GLYMA20G30820.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G052926_T02 (Zea mays), 5'ss of exon 6
GTTCATCACATGCTGTATCCTATGACAGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctctcagatttctccctttctcttctttccatccctattaacatttttgtgttcctagactttaac-taggtagcttgaggtta-tatttttgt
 | || || ||| | |||||||| ||||||||  | ||  ||||||||||     |  |||||| |||||| |||||||| |||||||| |||||||||||| ||||| ||   | | ||||  | ||| |     |   | |    | |   | |   ||    || |       || | || || |  |  ||   | | 
ATCCACCATATGATCTATCCTATAACAGTGGAGATTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagattttcct-gctctctctatctctttcaccacgcacgcgtgcacctggtatacattttctgattcccttacagattgcatgtgaatggtaaggtgg-

upper sequence: GLYMA20G30820.1 (Glycine max), 5'ss of exon 6
lower sequence: AT1G43190.1 (Arabidopsis thaliana), 5'ss of exon 6
GTTCATCACATGCTGTATCCTATGACAGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctc------tcagatttctccctttctcttctttccatccctattaac----------atttttgtgttcctagacttta----actaggtagcttgaggttatatttttgt---------------------------------------------------------------------
 | ||||||||||||||||| || || || || || ||| ||||||| ||||||||| |||||| ||| || ||| | || || || |||||||| ||||||||| |||||      ||   | |||| || |||||   ||| || | | ||| |          ||||    |||  |    || |    | | |     || |  | |||||  |||                                                                     
ATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGCTCGTCACTTTCCAGAAGTCTGCTGgtcagcttctccgcatttcttttctctctctctctctctcttctattcgttttagcttagagaattatttgaaagtttgtctgtttcatgttattggtctctttaaaataatattgctgttaaaactttgtatttgccatctaacagtttgatgattgttaactataagcttgtttgttgactatttag

upper sequence: GLYMA20G30820.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv18s0072g00310.t01 (Vitis vinifera), 5'ss of exon 5
GTTCATCACATGCTGTATCCTATGACAGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctctcagatttctccctttctcttctttccatccctattaacatttttgtgttcctagactttaactaggtagcttgaggttatatttttgt-
 |||||||| |||| || ||||| |||||||| |||||| ||||||| |||||||| ||||| | |||||| |||||||| || ||||||||||||||||||||| ||||   || |||||| |||| |||   ||    |  | |    || | |   ||| ||    |    |       |   |  ||  |   ||  
ATTCATCACCTGCTATACCCTATAACAGTGGAGGTGCTGCATCAAGTGTTTTCTCCTCATGGTTTTGTGGAGAAGATTGTCACGTTTCAGAAGTCAGCTGgtcagcttcttcaagttttctctctttatctctcttgtg-ctgtctctctatctcttaattcttaattctcctttcaactcttgaggactagctggatggt

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|193682699|gb|FK623419.1|FK623419
EST:     TTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTG                         GCTTTCAGGCTCTCATCCAGTATCAATCACGTCAGAGTGCTGTTGCGGCAA
genomic: TTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattct ... aactttgtagGCTTTCAGGCTCTCATCCAGTATCAATCACGTCAGAGTGCTGTTGCGGCAA
EST: gi|193579113|gb|FK536749.1|FK536749
EST:     TTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTG                         GCTTTCAGGCTCTCATCCAGTATCAATCACGTCAGAGTGCTGTTGCGGCAA
genomic: TTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattct ... aactttgtagGCTTTCAGGCTCTCATCCAGTATCAATCACGTCAGAGTGCTGTTGCGGCAA
EST: gi|208136236|gb|GD940091.1|GD940091
EST:     TTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTG                         GCTTTCAGGCTCTCATCCAGTATCAATCACGTCAGAGTGCTGTTGCAGCAA
genomic: TTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattct ... aactttgtagGCTTTCAGGCTCTCATCCAGTATCAATCACGTCAGAGTGCTGTTGCGGCAA
EST: gi|17400944|gb|BM177726.1|BM177726
EST:     CATTTCAGAAGTCAGCTG                         GCTTTCAGGCTCTCATCCAGTATCAATCACGTCAGAGTGCTGTTGCGGCAA
genomic: CATTTCAGAAGTCAGCTGgtcagattct ... aactttgtagGCTTTCAGGCTCTCATCCAGTATCAATCACGTCAGAGTGCTGTTGCGGCAA
EST: gi|151404880|gb|EV274694.1|EV274694
EST:     TTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTG                         GCTTTCAGGCTCTCATCCAGTATCAATCACGTCAGAGTGCTGTTGCGGCAA
genomic: TTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattct ... aactttgtagGCTTTCAGGCTCTCATCCAGTATCAATCACGTCAGAGTGCTGTTGCGGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCATCACATGCTGTATCCTATGACAGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctctcagatttctccctttctcttctttccatccctattaacatttttgtgttcctagactttaactaggtagcttgaggttatatttttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatccc