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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttctctctagtttgagctctattatttttctcaagagtcatgattgttttatgcagcttttaatttctgctttctgattcttctgtattgatgtctagGATCTCTTTACTATTGGCCTTGGCTGGATAATTTTTGGTGGGCTACCATTTGATTTT

Basic information

species Glycine max
transcript GLYMA17G32030.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G32030.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0008g05570.t01 (Vitis vinifera), 3'ss of exon 8
-ctttctctcta-gtttgagctctattatttttctcaagagtcatgattgttttatgcagcttttaatttctgctttctgattcttctgtattgatgtctagGATCTCTTTACTATTGGCCTTGGCTGGATAATTTTTGGTGGGCTACCATTTGATTTT
  | |||   || ||||   |||  || || | ||      |||  |     | |  | |     | | ||   |||   |||||| |||  |  | | |||||| | ||||| ||||| ||||||||||| |||||||| ||||| || |||||| ||
agtctctaattatgttttgcctcggtttttatactttcatttcaaaacatcgtcaccctgtacacattctcaaattttctattctt-tgtgctcct-tgtagGATTTGTTTACCATTGGACTTGGCTGGATGATTTTTGGGGGGCTTCCTTTTGATATT
















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|207755356|gb|GD729391.1|GD729391
EST:     CTAAATTCAGCTGTGACACAGACAATTTGTGGTAATCTGAAG                         GATCTCTTTACTATTGGCCTTGGCTGGATAATTTTTGGTGGGCTACCATTT
genomic: CTAAATTCAGCTGTGACACAGACAATTTGTGGTAATCTGAAGgtatgtatgc ... tgatgtctagGATCTCTTTACTATTGGCCTTGGCTGGATAATTTTTGGTGGGCTACCATTT
EST: gi|22933439|gb|BU550578.1|BU550578
EST:     ACACAACACTAAATTCAGCTGTGACACAGACAATTTGTGGTAATCTGAAG                         GATCTCTTTACTATTGGCCNNNGCTGGATAATTTTTGGTGGGCTACCATTT
genomic: ACACAACACTAAATTCAGCTGTGACACAGACAATTTGTGGTAATCTGAAGgtatgtatgc ... tgatgtctagGATCTCTTTACTATTGGCCTTGGCTGGATAATTTTTGGTGGGCTACCATTT
EST: gi|19270080|gb|BM886336.1|BM886336
EST:     ACACAACACTAAATTCAGCTGTGACACAGACAATTTGTGGTAATCTGAAG                         GATCTCTTTACTATTGGCCTTGGCTGGATAATTTTTGGTGGGCTACCATTT
genomic: ACACAACACTAAATTCAGCTGTGACACAGACAATTTGTGGTAATCTGAAGgtatgtatgc ... tgatgtctagGATCTCTTTACTATTGGCCTTGGCTGGATAATTTTTGGTGGGCTACCATTT
EST: gi|16105385|gb|BI893125.1|BI893125
EST:     ACACAACACTAAATTCAGCTGTGACACAGACAATTTGTGGTAATCTGAAG                         GATCTCTTTACTATTGGCCTTGGCTGGATAATTTTTGGTGGGCTACCATTT
genomic: ACACAACACTAAATTCAGCTGTGACACAGACAATTTGTGGTAATCTGAAGgtatgtatgc ... tgatgtctagGATCTCTTTACTATTGGCCTTGGCTGGATAATTTTTGGTGGGCTACCATTT
EST: gi|151397123|gb|EV266996.1|EV266996
EST:     ACACAACACTAAATTCAGCTGTGACACAGACAATTTGTGGTAATCTGAAG                         GATCTCTTTACTATTGGCCTTGGCTGGATAATTTTTGGTGGACTACCATTT
genomic: ACACAACACTAAATTCAGCTGTGACACAGACAATTTGTGGTAATCTGAAGgtatgtatgc ... tgatgtctagGATCTCTTTACTATTGGCCTTGGCTGGATAATTTTTGGTGGGCTACCATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttttatgcagcttttaatttctgctttctgattcttctgtattgatgtctagGATCTCTTTACTATTGGCCTTGGCTGGATAATTTTTGGTGGGCTACCATTTGATTTT
                                          tattgat  putative branch site (score: 3)
              ttttaatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttctctctagtttgagctctattatttttctcaagagtcatgattgttttatgcagcttttaatttctgctttctgattcttctgtattgatgtctagGATCTCTTTACTATTGGCCTTGGCTGGATAATTTTTGGTGGGCTACCATTTGATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - gtcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcagct