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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattaaattatcctactattaccttctaaaaattcagagtatgccatgatcaatgagttaactaaaattaatgttatacctctaatctgtcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCGAGTTACTCAATTATACACTGGTCGTCTTTAAATTCCAAGAGATCAGAAA

Basic information

species Glycine max
transcript GLYMA17G00740.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G00740.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0568g00010.t01 (Vitis vinifera), 3'ss of exon 4
gaattaaattatcctactattaccttctaaaa-attcagagtatgccatgatcaatgagtta--actaaaatt----aatgttatacctctaatctgtcat-ttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCGAGTTACTCAATTATACACTGGTCGTCTTTAAATTCCAAGAGATCAGAAA
        || |  | ||   |  ||    ||   |  |  |||  ||  ||   | | | |  | |   | |    | | ||||   |      ||   | |||||||||||||||||||||||| | ||||||||||||||||  || ||| | ||   ||  || || || || ||||| || |||| || |||||   | ||| 
--------ttcttttcctgcaatattagggaatgatttggatatatcaaaatgtgtaaataaccattctgacttctgagtattattgtttggtattggtgtattgcagTTGAGGAACTTGGTTTGGTCTACATCAAAGCATGATGTCTACCTTATGTCTCATTTTTCTATCATTCATTGGTCTTCGTTAAGTTGCAAGAAGACTGAAG
















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|193420877|gb|FK385830.1|FK385830
EST:     ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAA                         TTGAGGAACTTGGTTT
genomic: ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAAgtatgttagt ... tcatttgcagTTGAGGAACTTGGTTT
EST: gi|209697566|gb|BW660573.1|BW660573
EST:     ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAA                         TTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCG
genomic: ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAAgtatgttagt ... tcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCG
EST: gi|254340112|gb|GR858237.1|GR858237
EST:     ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAA                         TTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCG
genomic: ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAAgtatgttagt ... tcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCG
EST: gi|18735074|gb|BM528549.1|BM528549
EST:     ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAA                         TTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCG
genomic: ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAAgtatgttagt ... tcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCG
EST: gi|11412572|gb|BF424583.1|BF424583
EST:     CTGTGAAATCAACAATACTTCATTTCCAA                         TTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCG
genomic: CTGTGAAATCAACAATACTTCATTTCCAAgtatgttagt ... tcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCG
EST: gi|151404558|gb|EV274372.1|EV274372
EST:     ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAA                         TTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTC
genomic: ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAAgtatgttagt ... tcatttgcagTT-GAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTC
EST: gi|213607081|gb|DB966986.1|DB966986
EST:     ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAA                         TTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCG
genomic: ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAAgtatgttagt ... tcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCG
EST: gi|192317031|gb|FK007826.1|FK007826
EST:     ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAA                         TTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCG
genomic: ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAAgtatgttagt ... tcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgatcaatgagttaactaaaattaatgttatacctctaatctgtcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCGAGTTACTCAATTATACACTGGTCGTCTTTAAATTCCAAGAGATCAGAAA
       aatgagttaactaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaattaaattatcctactattaccttctaaaaattcagagtatgccatgatcaatgagttaactaaaattaatgttatacctctaatctgtcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCGAGTTACTCAATTATACACTGGTCGTCTTTAAATTCCAAGAGATCAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA