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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgccccggcagaattttgcacaactcaatttgtgccctaattggtcaatttctcttcaaaatcacggaattagggtattctctcacggtgtatggagggcagaaatctgatatatgttttttaatttttgtgtagAAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATCAATGCAGAGATTCGTCGTACTAAGGCTCGGTTGCTGGAGGAGGTTCCCA

Basic information

species Glycine max
transcript GLYMA10G05870.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G05870.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0040g02130.t01 (Vitis vinifera), 3'ss of exon 1
gtacgccccggcagaattttgcacaactcaatttgtgccctaattggtcaatttctcttcaaaatcacggaattagggtattctctcacggtgtatggagggcagaaatctgatatat---gttttttaatttttg---tgtagAAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATCAATGCAGAGATTCGTCGTACTAAGGCTCGGTTGCTGGAGGAGGTTCCCA
                                         |||| ||  |||| | |||   |  |           | || |   |      | |||||       | | || | |    ||||     |||||   || |||||||||| | ||| || || ||||||  ||  || || || || ||  | || || ||||||||||| || |||||||| |||||||||||||| || |
-----------------------------------gatttaaattagtagattttttttctggactatt---------tcttattggaaaacaaacggaggtttagggtttaatttgtccaattttgagggttttgatctgcagAAAGCAGATACTGCATCTAACGAGAAAAATAGAGCGTCTGCGGTTGCTTTGAACGCCGAGATTCGTCGGACCAAGGCTCGATTGCTGGAGGAGGTCCCTA
















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|209719210|gb|BW679776.1|BW679776
EST:     TTGCCAGACTCTACGCCTCCGTCGACGCCGACATCGAGGCCCTACTTCAG                         AAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATC
genomic: TTGCCAGACTCTACGCCTCCGTCGACGCCGACATCGAGGCCCTACTTCAGgtacgccccg ... ttttgtgtagAAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATC
EST: gi|26048180|gb|CA784745.1|CA784745
EST:     TTGCCAGACTCTACGCCTCCGTCGACGCCGACATCGAGGCCCTACTTCAG                         AAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATC
genomic: TTGCCAGACTCTACGCCTCCGTCGACGCCGACATCGAGGCCCTACTTCAGgtacgccccg ... ttttgtgtagAAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATC
EST: gi|298198162|gb|HO039701.1|HO039701
EST:     TTGCCAGACTCTACGCCTCCGTCGACGCCGACATCGAGGCCCTACTTCAG                         AAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATC
genomic: TTGCCAGACTCTACGCCTCCGTCGACGCCGACATCGAGGCCCTACTTCAGgtacgccccg ... ttttgtgtagAAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATC
EST: gi|26048411|gb|CA784901.1|CA784901
EST:     TTGCCAGACTCTACGCCTCCGTCGACGCCGACATCGAGGCCCTACTTCAG                         AAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATC
genomic: TTGCCAGACTCTACGCCTCCGTCGACGCCGACATCGAGGCCCTACTTCAGgtacgccccg ... ttttgtgtagAAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATC
EST: gi|21888729|gb|BQ741942.1|BQ741942
EST:     TTGCCAGACTCTACGCCTCCGTCGACGCCGACATCGAGGCCCTACTTCAG                         AAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATC
genomic: TTGCCAGACTCTACGCCTCCGTCGACGCCGACATCGAGGCCCTACTTCAGgtacgccccg ... ttttgtgtagAAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATC
EST: gi|9565687|gb|BE475196.1|BE475196
EST:     TTGCCAGACTCTACGCCTCCGTCGACGCCGACATCGAGGCCCTACTTCAG                         AAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATC
genomic: TTGCCAGACTCTACGCCTCCGTCGACGCCGACATCGAGGCCCTACTTCAGgtacgccccg ... ttttgtgtagAAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcacggtgtatggagggcagaaatctgatatatgttttttaatttttgtgtagAAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATCAATGCAGAGATTCGTCGTACTAAGGCTCGGTTGCTGGAGGAGGTTCCCA
                                      ttttaat  putative branch site (score: 3)
                                            tttttgt  CT-rich tract
                    agaaatctgatatatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgccccggcagaattttgcacaactcaatttgtgccctaattggtcaatttctcttcaaaatcacggaattagggtattctctcacggtgtatggagggcagaaatctgatatatgttttttaatttttgtgtagAAAGCAGAAAGTGCTTCCAAGGAGAAAGGTAAGGCATCAGCTGTAGCGATCAATGCAGAGATTCGTCGTACTAAGGCTCGGTTGCTGGAGGAGGTTCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG