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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaacctaacttacaactgttactcttgctactttaatgtagaatattggcagacaagaataagcactaataaatggcatttcctctcctatgttacagTCTATGCTTGTTTTCTTCAAACCAATCAAGTTTGCGATAGCATTCACTCTTGGTAATTTGCTTTCACTTGGAAG

Basic information

species Glycine max
transcript GLYMA16G33260.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G33260.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0130g00230.t01 (Vitis vinifera), 3'ss of exon 2
gaaaacctaactt-acaactgttactcttgctactttaatgtagaatattggcagacaagaataagcactaataaatggcattt--cctctcctatgttacagTCTATGCTTGTTTTCTTCAAACCAATCAAGTTTGCGATAGCATTCACTCTTGGTAATTTGCTTTCACTTGGAAG
     | |  ||  | || || |  |  |   |   |   |  | ||||| |  | |  ||| ||     | |        |||   || |||  ||| |||||| ||||||||||||||||| ||||||||||| | |||| |||||||  |||| ||||||||| ||||||| ||
---gtcatggctggaaaattggttttactatcaaactggagatggatattagtggccttgaaaaaatctaacttgcctatttttgttctttcccctgtgacagTCAATGCTTGTTTTCTTCAATCCAATCAAGTTCGGGATAACATTCACCTTTGGCAATTTGCTTGCACTTGGGAG
















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|18692719|gb|BM521567.1|BM521567
EST:     TATATGGTTTTGCCATATGCTTTGCTGCTGGATTAACTTGTACGCTATTG                         TCTATGCTTGTTTTCTTCAAACCAATCAAGTTTGCGATAGCATTCACTCTT
genomic: TATATGGTTTTGCCATATGCTTTGCTGCTGGATTAACTTGTACGCTATTGgtaagtttga ... tatgttacagTCTATGCTTGTTTTCTTCAAACCAATCAAGTTTGCGATAGCATTCACTCTT
EST: gi|192308015|gb|FG998998.1|FG998998
EST:     TATATGGTTTTGCCGTATGCTTTGCTGCTGGATTAACTTGTACGCTATTG                         TCTATGCTTGTTTTCTTCAAACCAATCAAGTTTGCGATAGCATTCACTCTT
genomic: TATATGGTTTTGCCATATGCTTTGCTGCTGGATTAACTTGTACGCTATTGgtaagtttga ... tatgttacagTCTATGCTTGTTTTCTTCAAACCAATCAAGTTTGCGATAGCATTCACTCTT
EST: gi|192306357|gb|FG995123.1|FG995123
EST:     TATATGGTTTTGCCATATGCTTTGCTGCTGGATTAACTTGTACGCTATTG                         TCTATGCTTGTTTTCTTCAAACCAATCAAGTTTGCGATAGCATTCACTCTT
genomic: TATATGGTTTTGCCATATGCTTTGCTGCTGGATTAACTTGTACGCTATTGgtaagtttga ... tatgttacagTCTATGCTTGTTTTCTTCAAACCAATCAAGTTTGCGATAGCATTCACTCTT
EST: gi|192308014|gb|FG998997.1|FG998997
EST:     TATATGGTTTTGCCGTATGCTTTGCTGCTGGATTAACTTGTACGCTATTG                         TCTATGCTTGTTTTCTTCAAACCAATCAAGTTTGCGATAGCATTCACTCTT
genomic: TATATGGTTTTGCCATATGCTTTGCTGCTGGATTAACTTGTACGCTATTGgtaagtttga ... tatgttacagTCTATGCTTGTTTTCTTCAAACCAATCAAGTTTGCGATAGCATTCACTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattggcagacaagaataagcactaataaatggcatttcctctcctatgttacagTCTATGCTTGTTTTCTTCAAACCAATCAAGTTTGCGATAGCATTCACTCTTGGTAATTTGCTTTCACTTGGAAG
                    cactaat  putative branch site (score: 2)
                                   tttcctctcctatgtt  putative PPT
                     actaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaacctaacttacaactgttactcttgctactttaatgtagaatattggcagacaagaataagcactaataaatggcatttcctctcctatgttacagTCTATGCTTGTTTTCTTCAAACCAATCAAGTTTGCGATAGCATTCACTCTTGGTAATTTGCTTTCACTTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
gaaaacc
- - - - - - - caactgt
- - - - - - - - - - - -ctcttgc
- - - - - - - - - - - - - - - - - - aatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - gcagaca