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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacattatctgatttgtggttgagttattaacattaaagaagaaaacaaagaaaaaaccaaaaggatttatcttttgattgccccaatttgtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCACAAGGAAGGAAAGCTCATTGGAACTCA

Basic information

species Glycine max
transcript GLYMA18G46390.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0046g03520.t01 (Vitis vinifera), 3'ss of exon 3
---tacatta-tctgatttgtggt-tgagttattaacattaaagaagaaaacaaagaaaaaaccaaaaggatttatcttttgattgccccaatttgtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCACAAGGAAGGAAAGCTCATTGGAACTCA-
   |    || ||||  ||||    |  |   ||  | ||| | | ||      |  |||      |  |  || ||||||||   ||  |  || | |  ||||||||   |||||||||||||||||||||| || |||||||| |||||||| || || || ||||||||||| || || 
agttgttgtactctgccttgttacattggcctttttctttatatatgattcttcatgaaat----tattgccttgtcttttga--accttatcttttgttgtgcagTTATTGATGACTATGATTATGTATTTTCCGAAAATGGTCTAGTGGCTCATAAAGATGGGAAGCTCATTGGCACCCAG
















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|213618074|gb|DB963707.1|DB963707
EST:     TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|192303883|gb|FG998235.1|FG998235
EST:     TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|213617059|gb|DB961539.1|DB961539
EST:     TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|16348803|gb|BI974398.1|BI974398
EST:     TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|192298879|gb|FG987624.1|FG987624
EST:     TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|193590717|gb|FK544590.1|FK544590
EST:     TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|298189249|gb|HO037652.1|HO037652
EST:     TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|192306997|gb|FG999988.1|FG999988
EST:     TTGTTGGGGG-TCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|209717163|gb|BW657626.1|BW657626
EST:     TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|197664690|gb|FD480363.1|FD480363
EST:     TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|193455949|gb|FK417042.1|FK417042
EST:     TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|192306982|gb|FG999987.1|FG999987
EST:     TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|6727118|gb|AW311472.1|AW311472
EST:     TGTTGGGGGTTCTGACCTTATAAAGATATCAGAACAACTTGGCAGCACCA                         GT-ACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCA
genomic: TGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCAC-Aggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCA
EST: gi|151394726|gb|EV264597.1|EV264597
EST:     GGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: GGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|192299912|gb|FG991786.1|FG991786
EST:     TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|151402943|gb|EV272756.1|EV272756
EST:     TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
genomic: TTGTTGGGGGTTCTGACCTTATAAAGATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCAC
EST: gi|31467953|gb|CD409981.1|CD409981
EST:     ATATCAGAGCAACTTGGCAGCACA                         GTTACCAATGACTATGATTATGTATTTTCTGAGAAT-GTCTTTGTGGCTCA
genomic: ATATCAGAGCAACTTGGCAGCACAggttagctat ... gtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTC-TTGTGGCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaagaaaaaaccaaaaggatttatcttttgattgccccaatttgtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCACAAGGAAGGAAAGCTCATTGGAACTCA
                           ttttgat  putative branch site (score: 4)
                                          tttgtct  putative PPT
                    atttatcttttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacattatctgatttgtggttgagttattaacattaaagaagaaaacaaagaaaaaaccaaaaggatttatcttttgattgccccaatttgtctgttgcaGTTACCAATGACTATGATTATGTATTTTCTGAGAATGGTCTTGTGGCTCACAAGGAAGGAAAGCTCATTGGAACTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - -gtggttg
- - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - accaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcccca