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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGACGGGTTGATCCAACTTTAGACATGGAAGCAGACCAAGGAGATGATTACACACATCTTCCTgtatggtgaatgaaactattcctcaatctcatataggaggttctttcacagcatgttttttcatattttatgcaaattcaccttttatagtgtaaaattg...

Basic information

species Glycine max
transcript GLYMA20G33940.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33940.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM5G870572_T03 (Zea mays), 5'ss of exon 11
GTTCGACGGGTTGATCCAACTTTAGACATGGAAGCAGACCAAGGAGATGATTACACACATCTTCCTgtatggtgaat----gaaactattcctcaatctcatataggaggttctttcacagcatgttttttcatatt--ttatgcaaattcaccttttatagtgtaaaattg------------------------------------------------
 |   ||| || |||||||| ||||||||||| ||||||   |||||||||||||  |||||||| ||||| |   |    | || |||     | | | | |    | ||  | ||     |  |||| ||||| |    ||      |  |  |||||| || |    |                                                 
ATAAAACGAGTCGATCCAACATTAGACATGGAGGCAGACACTGGAGATGATTACATTCATCTTCCGgtatgatttttttctgcaattatcttatatttttaaaacaaatgtggtctc----tagattttctcatactgagcatatttgcttgctgtttataatgaagtgcttatcctatgttgaaactactgctcaatcattatgtgtttggaccctcag

upper sequence: GLYMA20G33940.1 (Glycine max), 5'ss of exon 11
lower sequence: AT1G55750.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTCGACGGGTTGATCCAACTTTAGACATGGAAGCAGACCAAGGAGATGATTACACACATCTTCCTgtatggtgaatgaaactattcctcaatctcatataggaggttc---tttcacagca-tgttttttcatattttatgcaaattcaccttttatagtgtaaaattg
 || ||||||||||||||||| | |||||||| || ||||| ||||| || ||||| ||||||   ||| |   | |   |||     | ||     |  |  |  | |   || | || || || || || | |    |    ||| | |  || | | |||| |    
ATTAGACGGGTTGATCCAACTCTTGACATGGAGGCTGACCAGGGAGACGACTACACTCATCTTATGgtaagtcaactaccactgcatgtgaaaggtttggataatttccaaattgcgcaacaatggttgttgaaaggaaagttcaatgctcagttaacactgtaca----

upper sequence: GLYMA20G33940.1 (Glycine max), 5'ss of exon 11
lower sequence: AT3G61420.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTCGACGGGTTGATCCAACTTTAGACATGGAAGCAGACCAAGGAGATGATTACACACATCTTCCTgtatggtgaatgaaactattcctcaatctcatataggaggttctttcacagcatgttttttcatattttatgca-aattcaccttttatagtgtaaaattg------
 |  ||||||||||||||||| | |||||||| || ||| | |||||||| ||||| |||||     |||||| |   || ||||      ||     ||   |||||  || | |  ||  |||    |      || | || |  ||    |||   ||    |       
ATGAGACGGGTTGATCCAACTCTTGACATGGACGCTGACGAGGGAGATGACTACACCCATCT-----TATGgtaagccaa-ctatcaactcattctgcatca-aggtttattgaaacgataatttcaagttaacagtgtagaaatttccacagataaaataggtctctcatcg

upper sequence: GLYMA20G33940.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv19s0015g01390.t01 (Vitis vinifera), 5'ss of exon 11
GTTCGACGGGTTGATCCAACTTTAGACATGGAAGCAGACCAAGGAGATGATTACACACATCTTCCTgtatggtgaatgaaac---tattcctcaatctcatataggaggttctttcacagcatgttttttcatattttatgcaaattcaccttttatagtgtaaaattg--
 |  ||||||||||||||||||| |||||||| || ||||| || |||||||| |  |||||||| ||| | ||||  | ||   | |||  ||||||||| ||  |  |  ||  | |     | |||  |||    || | | ||      | | |   |    |    
ATCAGACGGGTTGATCCAACTTTGGACATGGAGGCTGACCAGGGGGATGATTATATGCATCTTCCGgtacgttgaacaacacccattttctacaatctcat-tataaactatttctataa----tctttaaataggagattctagtttgatactaagaaaattttgtgtac

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|6501824|gb|AW203258.1|AW203258
EST:     CAACTTTAGACATGGAAGCAGATCAAGGAGATGATTACACACATCTTCCT                         GATCATGGGATTTTCCGAGATGGTAGCAAGGATATATCTGAAGCCCAAAAT
genomic: CAACTTTAGACATGGAAGCAGACCAAGGAGATGATTACACACATCTTCCTgtatggtgaa ... tgatgataagGATCATGGGATTTTCCGAGACGGTAGCAAGGATATATCTGAAGCCCAAAAT
EST: gi|20449480|gb|BQ253604.1|BQ253604
EST:     CAACTTTAGACATGGAAGCAGATCAAGGAGATGATTACACACATCTTCCT                         GATCATGGGATTTTCCGAGATGGTAGCAAGGATATATCTGAAGCCCAAAAT
genomic: CAACTTTAGACATGGAAGCAGACCAAGGAGATGATTACACACATCTTCCTgtatggtgaa ... tgatgataagGATCATGGGATTTTCCGAGACGGTAGCAAGGATATATCTGAAGCCCAAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCGACGGGTTGATCCAACTTTAGACATGGAAGCAGACCAAGGAGATGATTACACACATCTTCCTgtatggtgaatgaaactattcctcaatctcatataggaggttctttcacagcatgttttttcatattttatgcaaattcaccttttatagtgtaaaattg

- - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - -  GAGATG