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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcatggaaaatctttttattttatcaggtaatgggtttaatttagccctttgaatattcgccacacattagctcattagagttttatgggaactcaattcttttccatagGCTGTGAATGATCTTTGCCTTTACAAAATGGGGGGAAATCTTTATCAACGAATTGAAAAGGAGTGTGAAGCACATATATCTGCAGCACTGCAGTCTTTAG

Basic information

species Glycine max
transcript GLYMA05G27240.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 2
------gtaatcatggaaa-atctttttattttatcaggtaatgggtttaatttagccctttgaatattcgccacacattagctcattagagttttatgggaactcaat-tcttttccatagGCTGTGAATGATCTTTGCCTTTACAAAATGGGGGGAAATCTTTATCAACGAATTGAAAAGGAGTGTGAAGCACATATATCTGCAGCACTGCAGTCTTTAG
        || |||  | | || | | ||| |    | ||| |   |||| |||  |  |||    | |    | |  || |   ||  ||   ||||   ||| |||  | || |   |||||||| |||||||| |||||  |||| ||||| |||||||| |||||||| |||||||||||||||||| ||||||||  ||||||| | || ||||| |
gttcattcaaccatatatatatatatatatatatatatgtatt---tttatttttcctttttctgaaatatttataagtt-gtctatctga---ttat--aaacccaacatattgtggttagGCTGTTAATGATCTCTGCCTCCACAAGATGGGTGGAAATCTCTATCAACGGATTGAAAAGGAGTGTGAATCACATATACGTGCAGCATTACAATCTTTGG
















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|209705496|gb|BW668074.1|BW668074
EST:     CTATATTCTTGAAGCAACCTGTTTCTTGTGACTTGGAGAATCTTTATCAG                         GCTGTGAATGATCTTTGCCTTTACAAAATGGGGGGAAATCTTTATCAACGA
genomic: CTATATTCTTGAAGCAACCTGTTTCTTGTGACTTGGAGAATCTTTATCAGgtaatcatgg ... ttttccatagGCTGTGAATGATCTTTGCCTTTACAAAATGGGGGGAAATCTTTATCAACGA
EST: gi|209698238|gb|BW667541.1|BW667541
EST:     CTATATTCTTGAAGCAACCTGTTTCTTGTGACTTGGAGAATCTTTATCAG                         GCTGTGAATGATCTTTGCCTTTACAAAATGGGGGGAAATCTTTATCAACGA
genomic: CTATATTCTTGAAGCAACCTGTTTCTTGTGACTTGGAGAATCTTTATCAGgtaatcatgg ... ttttccatagGCTGTGAATGATCTTTGCCTTTACAAAATGGGGGGAAATCTTTATCAACGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcgccacacattagctcattagagttttatgggaactcaattcttttccatagGCTGTGAATGATCTTTGCCTTTACAAAATGGGGGGAAATCTTTATCAACGAATTGAAAAGGAGTGTGAAGCACATATATCTGCAGCACTGCAGTCTTTAG
                                     ctcaattcttttcc  CT-rich tract
                                        aattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcatggaaaatctttttattttatcaggtaatgggtttaatttagccctttgaatattcgccacacattagctcattagagttttatgggaactcaattcttttccatagGCTGTGAATGATCTTTGCCTTTACAAAATGGGGGGAAATCTTTATCAACGAATTGAAAAGGAGTGTGAAGCACATATATCTGCAGCACTGCAGTCTTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG