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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggtaattgatgtatattgttcccattgctatgttactctaaatttttcacctttcattcccctgcatgatcactaattagttgttaacatgagaacagATTGTGGATGAATACAACCGTCTTCTTACATCTCAGTTGGAGACACAAAGACAA

Basic information

species Glycine max
transcript GLYMA17G12120.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G12120.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g55480.2 (Oryza sativa), 3'ss of exon 7
gtggtaattgatgtatattgttcccattgctatgttactctaaatttttcacctttcattcccctgcatgatcactaattagttgttaacatgagaacagATTGTGGATGAATACAACCGTCTTCTTACATCTCAGTTGGAGACACAAAGACAA
   ||||||| | ||   |     |||| |  | | |   |  |    |||  |  || ||   | | | |   |  ||  | | ||  |||   |||||||||||||||||||||||||||||||| |    ||  | || || || ||| | 
---gtaattgctttaagattcattcatttcagt-taatctttgacacctcat-tgccagtctggttcctcaaatcacatatgcttttctcat---aacagATTGTGGATGAATACAACCGTCTTCTTGCTAGCCAACTTGAAACTCAGAGAGAG

upper sequence: GLYMA17G12120.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g05600.t01 (Vitis vinifera), 3'ss of exon 6
gtggtaattgatgt-atattgttcccattg--ctatgttactctaaatttttcacctttcattcccctgcatgatca-ctaattagttgttaacatgagaacagATTGTGGATGAATACAACCGTCTTCTTACATCTCAGTTGGAGACACAAAGACAA
  | || || |||| ||  |  |   | ||   |||||||||   |   | | |  |||  |        |  |  |  | ||| ||  ||    ||  |||||||||||||||||||||||| ||||||| || || || |||| || |||||||||
--gctactttatgtgatgctcattagagtgatttatgttacttctatcctgtaatgtttactattgggataaaacaagttgatttgtcattgt--tgctaacagATTGTGGATGAATACAACCATCTTCTTGCAACTGAGATGGAAACTCAAAGACAA
















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|193339301|gb|FK305264.1|FK305264
EST:     GTGAAGATTTAGGAATTAATGGGGCCCTTTTCAACAGCAAAGTTGAAACG                         ATTGTGGATGAATACAACCGTCTTCTTACATCTCAGTTGGAGACACAAAGA
genomic: GTGAAGATTTAGGAATTAATGGGGCCCTTTTCAACAGCAAAGTTGAAACGgtatggttct ... atgagaacagATTGTGGATGAATACAACCGTCTTCTTACATCTCAGTTGGAGACACAAAGA
EST: gi|193368811|gb|FK335177.1|FK335177
EST:     GGGGCCCTTTTCAACAGCAAAGTTGAAACG                         ATTGTGGATGAATACAACCGTCTTCTTACATCTCAGTTGGAGACACAAAGA
genomic: GGGGCCCTTTTCAACAGCAAAGTTGAAACGgtatggttct ... atgagaacagATTGTGGATGAATACAACCGTCTTCTTACATCTCAGTTGGAGACACAAAGA
EST: gi|208318541|gb|GE111078.1|GE111078
EST:     GTGAAGATTTAGGAATTAATGGGGCCCTTTTCAACAGCAAAGTTGAAACG                         ATTGTGGATGAATACAACCGTCTTCTTACATCTCAGTTGGAGACACAAAGA
genomic: GTGAAGATTTAGGAATTAATGGGGCCCTTTTCAACAGCAAAGTTGAAACGgtatggttct ... atgagaacagATTGTGGATGAATACAACCGTCTTCTTACATCTCAGTTGGAGACACAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcacctttcattcccctgcatgatcactaattagttgttaacatgagaacagATTGTGGATGAATACAACCGTCTTCTTACATCTCAGTTGGAGACACAAAGACAA
                                      tgttaac  putative branch site (score: 2)
                              taattagttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggtaattgatgtatattgttcccattgctatgttactctaaatttttcacctttcattcccctgcatgatcactaattagttgttaacatgagaacagATTGTGGATGAATACAACCGTCTTCTTACATCTCAGTTGGAGACACAAAGACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - tgatgta
- - - - - - - - - - - -ccattgc