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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgcacagtatttgcagtatgaagttaaaagttctgcttctgaagtattttgtcgcacttgaatccattaattattgtaacacttgtttctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTTGGCAACCAGAATTTTCCTCCACCAAAGGGGAAGCCCATTGAAGAATCAG

Basic information

species Glycine max
transcript GLYMA0048S00280.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0048S00280.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0094g01420.t01 (Vitis vinifera), 3'ss of exon 3
gttgcacagtatttgcagta-tgaagttaaa-agttctgcttctgaagtattttgtcgcacttgaatccattaattattgtaacacttgtttctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTTGGCAACCAGAATTTTCCTCCACCAAAGGGGAAGCCCATTGAAGAATCAG
     |    |  ||||  | | || ||| | |  |    || ||   |   ||||    ||     | ||   |  || |     || |   ||| || |||| || |||||||||||| |||| ||||||||||||||||  ||||||||||| ||||| || || |||||| ||   || ||||| |||||| | ||||
--gaaaatacacctgcacaagttaaattatacaactaattttgtgctctgggttgtgtggctcatgactatctctgttttttttttttttcattttgtgaagAAAGGTACAAAACTCCGTATTGCTGATTTTGTCCATGGTGCGGATGGACTTGGAAACCAAAACTTCCCTCCATCAGCAGGAAAGCCAATTGAACAGTCAG
















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|192319150|gb|FK006906.1|FK006906
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
EST: gi|19054280|gb|BM732947.1|BM732947
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
EST: gi|254326906|gb|GR836515.1|GR836515
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
EST: gi|7685922|gb|AW756570.1|AW756570
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
EST: gi|9259144|gb|BE347291.1|BE347291
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATATTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
EST: gi|254346378|gb|GR856100.1|GR856100
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
EST: gi|298180188|gb|HO025403.1|HO025403
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
EST: gi|10709506|gb|BF009230.1|BF009230
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
EST: gi|192317205|gb|FK009792.1|FK009792
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
EST: gi|16997071|gb|BM086443.1|BM086443
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
EST: gi|192325277|gb|FK019148.1|FK019148
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
EST: gi|6071945|gb|AW101332.1|AW101332
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
EST: gi|5057387|gb|AI735863.1|AI735863
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
EST: gi|7685834|gb|AW756482.1|AW756482
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
EST: gi|192319151|gb|FK006907.1|FK006907
EST:     CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACT                         AATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT
genomic: CTGGGAGAACGGATATACCGGTGGCAGAAGGATCTCATGTAACTTCAACTgtaagtctgt ... ctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattttgtcgcacttgaatccattaattattgtaacacttgtttctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTTGGCAACCAGAATTTTCCTCCACCAAAGGGGAAGCCCATTGAAGAATCAG
                              ttgtaac  putative branch site (score: 2)
                                      cttgtttcttt  CT-rich tract
                      attaattattgtaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgcacagtatttgcagtatgaagttaaaagttctgcttctgaagtattttgtcgcacttgaatccattaattattgtaacacttgtttctttatgcagAATGGAACAAAACTCCGTGTTGCAGATTTTGTCCATGGTGTAGATGGACTTGGCAACCAGAATTTTCCTCCACCAAAGGGGAAGCCCATTGAAGAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- tgcacag
- - - - - - -tgcagta
- - - - - - - - - - - - - - - - - ctgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cacttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacttgt