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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAGgtgcctgcttttctaaattagataattgcttattggattttaatgtttgtttgtgtaatactcatgcttaacttagaatattgaaattacattaaataat...

Basic information

species Glycine max
transcript GLYMA20G18440.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G18440.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os02g13990.3 (Oryza sativa), 5'ss of exon 6
GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAGgtgcctgcttttctaaattagataat-tgcttattggattttaatgtttgtttgtgtaatactcatgcttaacttagaatattgaaattacattaaataat
||||||||||||||||||||||| ||||| |||||||| ||||||||||||||  |   |  | |   |||| |  |  ||||  |  | |||        |   | |    ||||   ||   ||  | || ||  || |  |||      
GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtcctttcgtttagctcctgcgctttgtacagtttggaacagctaactatgg-gctcacatttctttttcactactgtgatga--ttag-----

upper sequence: GLYMA20G18440.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv01s0150g00590.t01 (Vitis vinifera), 5'ss of exon 6
GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAGgtgcctgctttt-ctaaattagat---aattgcttattggattttaatgtttgtttgtgtaatactcatgcttaacttagaatattgaaattacattaaataat
|| || ||||||||||| |||||||||||||||||||| ||||||||||||||||   |||||  | |||||||     ||| | | |||  ||| ||||||| ||  | || |  | |  |  |  ||   ||||  |   | | ||   ||  
GCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAGgtgctgtcttttgtttaattagacttggatttcattttgtttttcaatgtttattctt-tatttttaacacc-atgttttcatatgaattgtgc-ttgggtag-

upper sequence: GLYMA20G18440.1 (Glycine max), 5'ss of exon 7
lower sequence: PP1S49_103V6.1 (Physcomitrella patens), 5'ss of exon 7
GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAGgtgc--ctgcttt-tctaaattagataattgcttattggattttaatgtttgtttg--tgtaatactcatgcttaacttagaatattgaaat-tacattaaataat--------------------------------------------------
 | || ||||  ||||||||||| ||||||||||| || |||||||||||||| |  |||||   | ||  ||||  |||||    ||   ||||| | |||  |||  | || | |      | |  | | || ||| |  | | |  |    |||                                                  
ACCGCTATTGCAAATTCTCAGACGCTTGAAGAGGTCGCCAGGCTTGAAAAGgtactactgctcggtatattttaggaaattg--agtttccttttactttttacttgattttagttcaatcattaagttcacaacattcagttatgccgtggtgaatttttatttggcacattgtgcatgcattgagatcttatttttcttttgcag

upper sequence: GLYMA20G18440.1 (Glycine max), 5'ss of exon 7
lower sequence: PP1S152_48V6.2 (Physcomitrella patens), 5'ss of exon 8
GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAGgtgcctgcttttctaaattagataattgcttattggattttaatgtttgttt-gtgtaatactcatgcttaacttagaatattgaaattacattaaataat------------------------------------------------
 ||||||| |  ||||| ||||| |||||||| ||||| ||||||||||||||  |    |||   || |  ||  |||   | || | |      ||  ||  ||| || | |  |   |    |  ||  ||    | |  ||      |                                                
ACTGCCATCGCAAATTCACAGACACTTGAAGAAGTTGCCAGGCTTGAAAAGgtagcactgtttgggaaatccatttttggaaactgaaatcactaattccttcagtgcaacatttttatgttgtatgcaacttttcgctcaacttcgtgggttttacaagtttgttgtgcatacattgaaatcgaaattatcttctgcag

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|17402141|gb|BM178923.1|BM178923
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAG                         GCATTGAAGTCTGGTCAGCTTCCTGCAGATTTAATAAGCTTGAGTGATAAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAGgtgcctgctt ... atgattgcagGCATTGAAGTCTGGTCAGCTTCCTGCAGATTTAATAAGCTTGAGTGATAAT
EST: gi|192305355|gb|FG994037.1|FG994037
EST:     CTGCCATTGTGAATTTTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAG                         GCATTGAAGTTTGGTCAGCTTCCTGCAGATTTAATAAGCCTGAGTGATAAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAGgtgcctgctt ... atgattgcagGCATTGAAGTCTGGTCAGCTTCCTGCAGATTTAATAAGCTTGAGTGATAAT
EST: gi|120494048|gb|EH222215.1|EH222215
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAG                         GCATTGAAGTCTGGTCAGCTTCCTGCAGATTTAATAAGCTTGAGTGATAAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAGgtgcctgctt ... atgattgcagGCATTGAAGTCTGGTCAGCTTCCTGCAGATTTAATAAGCTTGAGTGATAAT
EST: gi|16343914|gb|BI969509.1|BI969509
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAG                         GCATTGAAGTCTGGTCAGCTTCCTGCAGATTTAATAAGCTTGAGTGATAAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAGgtgcctgctt ... atgattgcagGCATTGAAGTCTGGTCAGCTTCCTGCAGATTTAATAAGCTTGAGTGATAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAGgtgcctgcttttctaaattagataattgcttattggattttaatgtttgtttgtgtaatactcatgcttaacttagaatattgaaattacattaaataat

- - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - AAGAGG