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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgttagatttattaatataatcttatagaaaacgaagcattaatgttagcaagtgcttaatatgtttttgatactcaatgattcaacag

Basic information

species Glycine max
transcript GLYMA10G04480.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 11
GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaa---tgttagatttattaatataatcttatagaaaacgaagcattaatgttagcaagtgcttaatatgtttttgatactcaatgattcaacag---
||||  |||||||| || ||||| |||||  |||||||||||||||| || |||||||| || ||  | |||||||    ||||    ||| |  |  |  |||   |     |      |     ||| | |  ||| |         |||     ||  ||         
GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatattagtggtgcatgcttgatgcttctgttagtcttcccgtaggaggcccttgagtaaacccagatctattattcttgcctgtctt

upper sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 11
GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgttagatttattaatataatcttatagaaaacgaagcatt----------aatgttagcaagtgcttaatatg--tttttgatactcaatgattcaacag
||| |||| |||||||| || || ||||| || ||||||||||||||||| ||||||||||||||  ||||||||||||  | |  | |  ||  |||   ||  |   |||    ||          ||    | ||    | ||||| |  || |||||    ||||||    |||
GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaaaacctttggatggaattcaatttatttcgagtgtttccaaaaaggaaaaaaaatcagaaacataatacgagttgttgatcacaaatgatattgcag
















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|192311647|gb|FK004866.1|FK004866
EST:     TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
genomic: TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
EST: gi|17021495|gb|BM092529.1|BM092529
EST:     TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
genomic: TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
EST: gi|4260094|gb|AI416590.1|AI416590
EST:     AGAATATTGAAG                         GAAAGTGGTATGGCATTAATANCGGCTGAAGATTTAGATGATGCAGCTCAG
genomic: AGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
EST: gi|192308760|gb|FG999785.1|FG999785
EST:     TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
genomic: TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
EST: gi|254325002|gb|GR834427.1|GR834427
EST:     TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGA-GATTTAGATGATGCAGCTCAG
genomic: TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
EST: gi|17964783|gb|BM271512.1|BM271512
EST:     TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
genomic: TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
EST: gi|298179372|gb|HO027843.1|HO027843
EST:     TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGAA
genomic: TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAA
EST: gi|18721747|gb|BM523360.1|BM523360
EST:     TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
genomic: TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
EST: gi|7326644|gb|AW620442.1|AW620442
EST:     TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
genomic: TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
EST: gi|51336677|gb|CO980543.1|CO980543
EST:     TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
genomic: TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
EST: gi|105633578|gb|DW246941.1|DW246941
EST:     TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
genomic: TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
EST: gi|151406201|gb|EV276016.1|EV276016
EST:     TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
genomic: TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
EST: gi|21600688|gb|BQ611019.1|BQ611019
EST:     GTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
genomic: GTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
EST: gi|6727069|gb|AW311423.1|AW311423
EST:     GTTCGTCTGGAATGCACCAATGTTGATCAANGGAAAA-GAATATTGGAAG                         GAA-GTGGTATGGCATTAATAACGGCTGGAGATATAGATGATGCAGCT
genomic: GTTCGTCTGGAAGGCACCAATGTTGATCAA-GGAAAAAGAATATTG-AAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCT
EST: gi|12689320|gb|BG155656.1|BG155656
EST:     AGTTCGTCTGGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
genomic: AGTTCGTCT-GGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
EST: gi|193491469|gb|FK455643.1|FK455643
EST:     ACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
genomic: ACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG
EST: gi|22523849|gb|BU082660.1|BU082660
EST:     TAGGTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG                         GAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCACCTCAT
genomic: TAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgtta ... gattcaacagGAAAGTGGTATGGCATTAATAACGGCTGAAGATTTAGATGATGCAGCTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgttagatttattaatataatcttatagaaaacgaagcattaatgttagcaagtgcttaatatgtttttgatactcaatgattcaacag

- - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG