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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATGATACATACCCACCATGGGCACATGGTCCTGGCTATGTTATCTCACGAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAGgtaagaatttcttctttcccatcatgggatgggggataaaaaattatgtgcttattttagaatcttttggataattcaaggatatgcttcttaagttttt...

Basic information

species Glycine max
transcript GLYMA17G04230.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G04230.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv05s0020g00400.t01 (Vitis vinifera), 5'ss of exon 7
CCATGATACATACCCACCATGGGCACATGGTCCTGGCTATGTTATCTCACGAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAGgtaagaatttcttctttccca--tcatgggatgggggataaaaaattatgtgctt--attttagaatcttttggataattcaaggatatgcttcttaagttttt
 | |||||| |||||||||||||| |||||||| || ||  | || || |||||||| |||||||| ||||| || | ||||||||||||| | ||| |||||||| || || ||| |  |  ||||  |     |        || |||| | |  ||   | |   |||    ||||        | ||| | |   |    
ACGTGATACGTACCCACCATGGGCCCATGGTCCAGGTTACATCATATCCCGAGACATTGCAAAATTCATTGTTCAAGGCCACCAAGAAAGAGACCTCCAGgtaagagttactgcttacaaagttcataagcaactgtcatgttcatcatgtccctccatgccaaatggtttcacctaatattcatggaagctccctctct----
















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|6719881|gb|AW307528.1|AW307528
EST:     GAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAG                         CTCTTTAAATTAGAAGATGTTGCCATGGGCATATGGATTGAACAGTTCAAG
genomic: GAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAGgtaagaattt ... ttattcttagCTCTTTAAATTAGAAGATGTTGCCATGGGCATATGGATTGAACAGTTCAAG
EST: gi|105633397|gb|DW246760.1|DW246760
EST:     GAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAG                         CTCTTTAAATTAGAAGATGTTGCCATGGGCATATGGATTGAACAGTTCAAG
genomic: GAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAGgtaagaattt ... ttattcttagCTCTTTAAATTAGAAGATGTTGCCATGGGCATATGGATTGAACAGTTCAAG
EST: gi|254323159|gb|GR835767.1|GR835767
EST:     GAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAG                         CTCTTTAAATTAGAAGATGTTGCCATGGGCATATGGATTGAACAGTTCAAG
genomic: GAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAGgtaagaattt ... ttattcttagCTCTTTAAATTAGAAGATGTTGCCATGGGCATATGGATTGAACAGTTCAAG
EST: gi|21479921|gb|BQ576604.1|BQ576604
EST:     GAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAG                         CTCTTTAAATTAGAAGATGTTGCCATGGGCATATGGATTGAACAGTTCAAG
genomic: GAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAGgtaagaattt ... ttattcttagCTCTTTAAATTAGAAGATGTTGCCATGGGCATATGGATTGAACAGTTCAAG
EST: gi|18692808|gb|BM521656.1|BM521656
EST:     GAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAG                         CTCTTTAAATTAGAAGATGTTGCCATGGGCATATGGATTGAACAGTTCAAG
genomic: GAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAGgtaagaattt ... ttattcttagCTCTTTAAATTAGAAGATGTTGCCATGGGCATATGGATTGAACAGTTCAAG
EST: gi|254323158|gb|GR835766.1|GR835766
EST:     GAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAG                         CTCTTTAAATTAGAAGATGTTGCCATGGGCATATGGATTGAACAGTTCAAG
genomic: GAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAGgtaagaattt ... ttattcttagCTCTTTAAATTAGAAGATGTTGCCATGGGCATATGGATTGAACAGTTCAAG
EST: gi|11688853|gb|BF596529.1|BF596529
EST:     GAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAG                         CTCTTTAAATTAGAAGATGTTGCCATGGGCATATGGATTGAACAGTTCAAG
genomic: GAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAGgtaagaattt ... ttattcttagCTCTTTAAATTAGAAGATGTTGCCATGGGCATATGGATTGAACAGTTCAAG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATGATACATACCCACCATGGGCACATGGTCCTGGCTATGTTATCTCACGAGACATAGCAAAATTTATTGTCCATGCCCACCAAGAAAGAAAACTCAAGgtaagaatttcttctttcccatcatgggatgggggataaaaaattatgtgcttattttagaatcttttggataattcaaggatatgcttcttaagttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggataaaa