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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactagtctggtatccaatcaaatacataacaattttgtacacctcagagctatcacttgttattgtcttaccaattttgttttgtaattctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTGATAGAACTCATCCGGAATGGAAAAGTAGAAGAAGCGCTAGAGTTTGCCC

Basic information

species Glycine max
transcript GLYMA15G07570.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G07570.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 9
aactagtctggtatccaatcaaatacataacaatt-ttgtacacctcagagctatcacttgttattgtcttaccaattttgt----tttgtaattctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTGATAGAACTCATCCGGAATGGAAAAGTAGAAGAAGCGCTAGAGTTTGCCC
      |   | |||  |  |||| ||||     | || |    |  | | || |       |  ||    || || ||| |    ||||   |||| | |||||||| | || ||||| |||||| ||||||||||||| ||||||||| | ||||||||||| || ||||||||||||||||| || || || |||||||| |
-----ttagagaatcacagaaaattcatatttgctgttatggttcctataactttggacatctcatgagccacaaaatttatcctttttggttttctttatgcagATATTAGATACAAACCCCCAACTATTTTTCCATCTCCAACAGCAAAGGTTGATAGAACTGATTCGGAATGGAAAAGTAGATGAGGCTCTGGAGTTTGCTC
















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|193555708|gb|FK513255.1|FK513255
EST:     GTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAG                         ATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
genomic: GTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAGgtaggcttct ... ctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
EST: gi|151408269|gb|EV278077.1|EV278077
EST:     GTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAG                         ATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
genomic: GTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAGgtaggcttct ... ctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
EST: gi|38193470|gb|CF922676.1|CF922676
EST:     ACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAG                         ATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
genomic: ACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAGgtaggcttct ... ctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
EST: gi|9819896|gb|BE555339.1|BE555339
EST:     GTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAG                         ATACTGGACACGNATCCCCCATTATTTGTCCATCTTCAACAGCAACGATTG
genomic: GTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAGgtaggcttct ... ctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
EST: gi|208037374|gb|GD835303.1|GD835303
EST:     GATGCAATTGAAAAAGTGAATGACTTAAATCCGGAG                         ATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
genomic: GATGCAATTGAAAAAGTGAATGACTTAAATCCAGAGgtaggcttct ... ctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
EST: gi|192328969|gb|FK021072.1|FK021072
EST:     GTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAG                         ATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
genomic: GTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAGgtaggcttct ... ctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
EST: gi|208317059|gb|GE111500.1|GE111500
EST:     AATTGAAAAAGTGAATGACTTAAATCCGGAG                         ATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
genomic: AATTGAAAAAGTGAATGACTTAAATCCAGAGgtaggcttct ... ctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
EST: gi|22928038|gb|BU545177.1|BU545177
EST:     TTGAAAAAGTGAATGACTTAAATCCAGAG                         ATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
genomic: TTGAAAAAGTGAATGACTTAAATCCAGAGgtaggcttct ... ctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
EST: gi|193719536|gb|FK650872.1|FK650872
EST:     GTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAG                         ATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
genomic: GTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAGgtaggcttct ... ctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
EST: gi|15812571|gb|BI784846.1|BI784846
EST:     GTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAG                         ATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
genomic: GTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAGgtaggcttct ... ctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG
EST: gi|192297765|gb|FG989971.1|FG989971
EST:     GTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAG                         ATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAATGATTG
genomic: GTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCCAGAGgtaggcttct ... ctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagagctatcacttgttattgtcttaccaattttgttttgtaattctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTGATAGAACTCATCCGGAATGGAAAAGTAGAAGAAGCGCTAGAGTTTGCCC
                    gtcttac  putative branch site (score: 3)
                                           ttctgtct  putative PPT
                            aattttgttttgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactagtctggtatccaatcaaatacataacaattttgtacacctcagagctatcacttgttattgtcttaccaattttgttttgtaattctgtctgcagATACTGGACACAAATCCCCAATTATTTTTCCATCTTCAACAGCAACGATTGATAGAACTCATCCGGAATGGAAAAGTAGAAGAAGCGCTAGAGTTTGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC