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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgctgtaatctatatctgcttttcatttatttctgtattgtttcaattttttgcatcagtcaacatgcccttgatgttggtttcttattctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTTGTAATGAACCCACAGAATGGTTTGACAATTAAACCATTCAGGAAGGCTC

Basic information

species Glycine max
transcript GLYMA05G30160.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30160.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g65450.1 (Oryza sativa), 3'ss of exon 5
attgctgtaatctatatctgcttttcatttatttctgt-attgtttcaattttttgcatcagtcaacatgcccttgatgttggtttcttattctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTTGTAATGAACCCACAGAATGGTTTGACAATTAAACCATTCAGGAAGGCTC---
                  |  |  |    |  | |||| | | | | | |  ||  |||      |  ||| | |    |  ||||||| |  |||    |   |||||||   |||| || ||||||||||||||||| ||||| || ||||| ||||| |||||||||||| |    || ||||||| || || | | |   
----------------gttagtagtggcgtggtactgtgaatttgtgactgattctcattgaattatttgctcattgcttctgtttctt-tcatat----gcagTACAATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTCATGAATCCACAGAATGGTCTTGTGATCAAACCATACAAGAGGACCCATT

upper sequence: GLYMA05G30160.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0035g00640.t01 (Vitis vinifera), 3'ss of exon 5
----attgctgtaatctatatctgcttttcatttatttctgtattgtttcaattttttgcatcagtcaacatgcccttgatgttggtttcttattctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTTGTAATGAACCCACAGAATGGTTTGACAATTAAACCATTCAGGAAGGCTC
    | |||| ||    | ||    || |    | ||||| | | |   ||||  | | |   | |  |||      || || |   || ||||| |  | |||||||||| | |   ||| || |||||||||||||||||| ||||||||||||| |||||||||||||| ||||||||||| || ||||||||||||||||
ttcaaatgctatatagaaaattgaattattgcatttttct-tgtgggcccaatgatcttc-ctacttgacaatagactggtggtatcttgttatttt--tgcagTTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTTGTGATGAACCCACAGAACGGTTTGACAATCAAGCCATTCAGGAAGGCTC
















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|151393341|gb|EV263216.1|EV263216
EST:     GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAG                         TTCTACAATGCTTCAAATACTATCATGTTTGATGACCTT
genomic: GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtataattat ... tctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTT
EST: gi|208295827|gb|GE092202.1|GE092202
EST:     GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAG                         TTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
genomic: GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtataattat ... tctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
EST: gi|192305353|gb|FG994035.1|FG994035
EST:     GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAG                         TTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
genomic: GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtataattat ... tctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
EST: gi|192305352|gb|FG994034.1|FG994034
EST:     GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAG                         TTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
genomic: GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtataattat ... tctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
EST: gi|7685022|gb|AW755670.1|AW755670
EST:     GATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAG                         TTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
genomic: GATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtataattat ... tctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattttttgcatcagtcaacatgcccttgatgttggtttcttattctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTTGTAATGAACCCACAGAATGGTTTGACAATTAAACCATTCAGGAAGGCTC
                         ccttgat  putative branch site (score: 5)
                                     tttcttattctatttc  putative PPT
                                     tttcttattctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgctgtaatctatatctgcttttcatttatttctgtattgtttcaattttttgcatcagtcaacatgcccttgatgttggtttcttattctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTTGTAATGAACCCACAGAATGGTTTGACAATTAAACCATTCAGGAAGGCTC

- tgctgta
- - - - - - - - tctgctt
- - - - - - - - - - - - - - - - ttctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgttg