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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaaacaaacactttcacgattcagccaaaacccaaaaaaacactttttttttttatgttccacaaaatcacgggcaatcgccaatttcgtttctttcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAGAGAGCGTATTTTGAGTCGCTGGCACTGAAAGAAGAGGGTCGTTTAATCC

Basic information

species Glycine max
transcript GLYMA20G26580.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G26580.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0091g00100.t01 (Vitis vinifera), 3'ss of exon 1
gtaacaaacaaacactttcacgattcagccaaaacccaaaaaaacactttttttttttatgttccacaaaatcacgggcaatcgccaatttcgtt-tctttcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAGAGAGCGTATTTTGAGTCGCTGGCACTGAAAGAAGAGGGTCGTTTAATCC
    || |   | | | |  | || ||   | | |    | ||    ||   |   |  |  |   | | | |    | ||      || | ||| | ||    ||  ||||  |||||||| | ||| | ||||||||||||||||| |||||||||||  | |||||||||||  ||  |||  ||| |||  || |||| |    | 
----catatctagaatatt-ctatacaaatatagctgttataacagattaaataaatgctagtatgctagaactgttgtaa-----gatgtggttgtgttgagagtgcagGCGTTGCCGTACATACGTAGTATAGGGGAATCGTGGCCGATGACGAAGGACCGGGCGTATTTTGAAGCGACGGCTTTGAGAGAGCAGCGTCGCTGGTGCT

upper sequence: GLYMA20G26580.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0091g00080.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------gtaacaaacaaacactttcacgattcagccaaaacccaa----aaaaacactttttttttttatgttccacaaaatcacg-ggcaatcgccaatttcgtttctttcttg--tatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAGAGAGCGTATTTTGAGTCGCTGGCACTGAAAGAAGAGGGTCGTTTAATCC
                           | |||||   | | | | ||     |   |   |   |      ||  | |||   |  || ||      |     | | | |  | |  |  |  | || | |   |  |  ||||  |||||||| | ||||| ||||||||||||||||| |||||||||||  | |||||||||||  ||  |||| ||| |||  || |||| |    | 
gtacaaattttgattcataacggcacctcacaaattcagattcttactgaaaaaaaatggcttcactgtggaagaattttaagtgcttgtgaaggttaggtcaaagtgactgttgtaagatgtggttgtgttgagagtgcagGCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAACGGGCGTATTTTGAAGCGACGGCATTGAGAGAGCAGCGTCGCTGGTGCT
















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|6567066|gb|AW234693.1|AW234693
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|18040792|gb|BM309086.1|BM309086
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|209713483|gb|BW679273.1|BW679273
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|192324081|gb|FK019372.1|FK019372
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|209726974|gb|BW680293.1|BW680293
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|14259302|gb|BG882210.1|BG882210
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|5820204|gb|AI988410.1|AI988410
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|298181549|gb|HO025724.1|HO025724
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|213594296|gb|DB969974.1|DB969974
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|20814789|gb|BQ299267.1|BQ299267
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|192298387|gb|FG988433.1|FG988433
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|8825853|gb|BE209583.1|BE209583
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|10710408|gb|BF010099.1|BF010099
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|151395513|gb|EV265390.1|EV265390
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|298165118|gb|HO011167.1|HO011167
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
EST: gi|298191511|gb|HO038990.1|HO038990
EST:     ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAG                         GCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG
genomic: ACTTCGTCTTCATTGTTTCCAACCCCGCAGGTTCTTTTGTCATCAAACAGgtaacaaaca ... tcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatgttccacaaaatcacgggcaatcgccaatttcgtttctttcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAGAGAGCGTATTTTGAGTCGCTGGCACTGAAAGAAGAGGGTCGTTTAATCC
                                  tttcgtttctttcttg  CT-rich tract
           acaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaaacaaacactttcacgattcagccaaaacccaaaaaaacactttttttttttatgttccacaaaatcacgggcaatcgccaatttcgtttctttcttgtatagGCTCTGCCGTACGTTCGTTGCATAGGGGAATCGTGGCCTATGACGAAGGAGAGAGCGTATTTTGAGTCGCTGGCACTGAAAGAAGAGGGTCGTTTAATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG