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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacatgttgcttggtttgacacagtagagactcattcatctgaattagttcttgtattttctataatttaggaaattgattatgttttccttggttttaagttaagttggttgtgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTGATGGAAGACAAGAAGAGCCTTGCTTCATCTGAAGAGCGTTCTCAGATAA

Basic information

species Glycine max
transcript GLYMA09G33160.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33160.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 8
gtaaaacatgttgcttggtttgacacagtagagactcattcatctgaattagttcttgtattttctataatttaggaaattgattatgtt--ttccttggttttaagt-taagttggttgtgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTGATGGAAGACAAGAAGAGCCTTGCTTCATCTGAAGAGCGTTCTCAGATAA
                   |||  |   || | |||  |  || |   | |  ||    |    |   ||  |  |||||| ||| || |  ||||   ||| ||| | |||  ||||    | |  ||||| |||||||| |  || ||||||||||| || || ||||| ||||| || ||||||||||| |||||||||||||| || || || ||  | || || |
------------------gttgctattata-atacttctctatat---tcaactccataaagccccccaaact--gaaatttattctgctgtttcccaagttctaactataaaatggtaacatgtc-cagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTAATGGAAGACAAAAAGAGCCTTGCTTCTTCAGATGAACGAGCCCAAATTA
















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|151397506|gb|EV267379.1|EV267379
EST:     CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAG                         -TCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAA
genomic: CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAGgtaaaacatg ... tgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAA
EST: gi|17964389|gb|BM271125.1|BM271125
EST:     CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAG                         GTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
genomic: CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAGgtaaaacatg ... tgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
EST: gi|58022401|gb|CX709142.1|CX709142
EST:     CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAG                         GTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
genomic: CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAGgtaaaacatg ... tgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
EST: gi|12496084|gb|BG046886.1|BG046886
EST:     AGCTATGGGATTTGACAATAGCACTCGTTTATATC-TGCCTTCTCACAGG                         GTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAA-TATNTTCNTC
genomic: AGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCC-TCTCACAAGgtaaaacatg ... tgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTAT-TTCCTC
EST: gi|21678323|gb|BQ630674.1|BQ630674
EST:     CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAG                         GTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
genomic: CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAGgtaaaacatg ... tgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
EST: gi|57574111|gb|CX547086.1|CX547086
EST:     CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAG                         GTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
genomic: CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAGgtaaaacatg ... tgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
EST: gi|19053704|gb|BM732371.1|BM732371
EST:     CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAG                         GTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
genomic: CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAGgtaaaacatg ... tgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
EST: gi|27425911|gb|CA937431.1|CA937431
EST:     CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAG                         GTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
genomic: CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAGgtaaaacatg ... tgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
EST: gi|193719450|gb|FK651404.1|FK651404
EST:     CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAG                         GTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
genomic: CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAGgtaaaacatg ... tgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
EST: gi|18732773|gb|BM527240.1|BM527240
EST:     CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAG                         GTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
genomic: CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAGgtaaaacatg ... tgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
EST: gi|208103902|gb|GD906847.1|GD906847
EST:     CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAG                         GTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
genomic: CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAGgtaaaacatg ... tgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
EST: gi|192308464|gb|FK000932.1|FK000932
EST:     CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAG                         GTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
genomic: CAGCTATGGGATTTGACAATAGCACTCGTTTATATCTTGCCTCTCACAAGgtaaaacatg ... tgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
EST: gi|8286203|gb|BE023762.1|BE023762
EST:     CTCGTTTATATCTTGCCTCTCACAAG                         GTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG
genomic: CTCGTTTATATCTTGCCTCTCACAAGgtaaaacatg ... tgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggaaattgattatgttttccttggttttaagttaagttggttgtgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTGATGGAAGACAAGAAGAGCCTTGCTTCATCTGAAGAGCGTTCTCAGATAA
     aattgat  putative branch site (score: 4)
                                             tgtttttc  putative PPT
     aattgattatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacatgttgcttggtttgacacagtagagactcattcatctgaattagttcttgtattttctataatttaggaaattgattatgttttccttggttttaagttaagttggttgtgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTGATGGAAGACAAGAAGAGCCTTGCTTCATCTGAAGAGCGTTCTCAGATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA