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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgatggtgtgctagttgatatttttaatgaattttctggtattttggttttctcaatattctgctgtgactaaagtttatattttatactgaaactgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG

Basic information

species Glycine max
transcript GLYMA10G42940.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 3
gtaatgatggtgtgctagttgatatttttaatgaattttctg-gtattttggttttctcaatattctgctgtgactaaagtttatattttatactgaaactgcatc---agGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG
||    |  || | ||     ||||  |  || | |    ||   ||||||     |||| | | ||    |   ||   ||| |   ||    || |  | ||||   |||| || || |  ||||| ||||| || || ||  | |||||||| || ||||| ||||| ||||| || || |||||||| |||||||||||||| |||
gtgtgtacagttttct--ccaatatgat-gataactaccatgtagattttgaacagctcagtctgctagcctc-ttatgctttgttcctttgcttgcatatccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAG

upper sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 4
gtaatgatggtgtgctagttgatatttttaatgaattttctggtattttggttttctcaatattctgctgtgactaaagtttatattttatactgaaactgcatc-agGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG
                            || ||   ||||     || |   |||   ||| ||||   ||  |    ||||     | ||||||        || |||| || ||||  ||||| ||||| ||||| ||| | || ||||||||||| || ||||| |||||||| || |||||||| || |||||||||||||||
---------------------------gtattggtgtttccatctttct--cttttataatgttct--cgtcccatgggtttcctgatgatactgctttcctctctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG

upper sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 3
gtaatgatggtgtgctagttgatatttttaatgaat--tttctggtattttggttttctcaatattctgctgtgactaaagtttatattttatactgaaactgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG
    |  |  |    || ||  |||||||| | | |  |||||| |   |  | ||||    | ||| |     | | |  |  ||  |||    |  || |||| ||||||||||||| |||||||||||| ||||||||||| ||||||||||| ||||| ||||| ||||| ||||| ||||||||||| ||||| ||||| |||
---gtattcctcacttatttagtatttttatttattcctttctgattcatatgatttccatctgttcagaatctattga--tcaatgattttctttctaattgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG

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|120533616|gb|EH261749.1|EH261749
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|120533425|gb|EH261558.1|EH261558
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|209697688|gb|BW655589.1|BW655589
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|120533188|gb|EH261321.1|EH261321
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|208058325|gb|GD856858.1|GD856858
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|13478635|gb|BG508033.1|BG508033
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|120532915|gb|EH261048.1|EH261048
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|120533316|gb|EH261449.1|EH261449
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|213596831|gb|DB964094.1|DB964094
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|120533627|gb|EH261760.1|EH261760
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|213591852|gb|DB973417.1|DB973417
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|19053577|gb|BM732244.1|BM732244
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|16346337|gb|BI971932.1|BI971932
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|209727398|gb|BW669851.1|BW669851
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGATAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|120533687|gb|EH261820.1|EH261820
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
EST: gi|213595962|gb|DB955998.1|DB955998
EST:     GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAG                         GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT
genomic: GAACTGTATCTGGAGTTGCTGGACCATTGGTCATTCTTGACAAAGTTAAGgtaatgatgg ... actgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctcaatattctgctgtgactaaagtttatattttatactgaaactgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG
                   gactaaa  putative branch site (score: 2)
                      taaagtttatatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgatggtgtgctagttgatatttttaatgaattttctggtattttggttttctcaatattctgctgtgactaaagtttatattttatactgaaactgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT