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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacttaatatttgtttattattttatttatgcctttggtatggcatatgaatgattaaatatgcttttcctgtgagtgtaaaccttgacctatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG

Basic information

species Glycine max
transcript GLYMA07G06590.1
intron # 3
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G06590.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------tacttaatattt---gtttattattttatttatgcctttggtatggcatatgaatgattaaatatgcttttcctgtg--------agtgtaaaccttgacctatttact-agAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG
                                                               | |||   | |    |  |||  |  | ||  || |||| |     | |     | ||||  |  ||  ||   |          | ||||   ||| |   || | || ||| ||||||||||||  ||||||||||  ||||||| || ||  | || |||||| |||||||||| |||||| | | ||||||||||||||| ||||| |
gtatccttcaaatttattatttggtgacttcttgttgggtttcaactctagcctaccccaacttgcttgggactaaaaggctatgttgatgttgttgtcttttgatcatcctcctgcttattattttggcactttaagcattggcggcattgtatctcttaataaatctccttagACCAACAAGGACATCATTGCACAAATCGTATCTGCAAGTATCACGGGTGATATTATTCTTGCTGCTGCATATTCCCGTGAGCTGCCACGATACGGTCTAG

upper sequence: GLYMA07G06590.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G163081_T04 (Zea mays), 3'ss of exon 3
-tacttaatatttgttt-attattttatttatgcct-ttggtatggcatatgaatgattaaatatgcttttcctgtgagtgtaaaccttgacctatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG
 ||     |  || ||| |  || |  ||| | ||| ||| ||||| |  |  |    |  | | || | |  |||   | | |||    |  ||||   |||| ||||||||||||   ||| ||||| ||||||||||| || || || ||||| ||||||||| | || ||  | |||||| ||||||||||||||||||
gtatcctttgattatttgaccatctggtttctacctattgctatggtactttga--gctccagaagcatatattgtatctcttaact---agatattc-ttagACCAACAAGGACATCACTGCCCAAATCATATCTGCTAGTATAGCGGGTGATATGGTTCTTGCTTCTGCCTACTCGCATGAGTTGCCACGATATGGTCTTG

upper sequence: GLYMA07G06590.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G815894_T03 (Zea mays), 3'ss of exon 3
------------tacttaat-atttgtttattattttatttatgcctttggtatg-gcatatga-----atgattaaatatgcttttcctgtgagtgtaaaccttgaccta--tttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG
            | ||| || ||||||||  | | || ||||  | | |||| |  || ||| |      |  || |       |  | |   | ||||   ||| ||      |   |||| ||||||||||||    |||||||| || |||||||| || || || ||||| ||||||||| | || ||  | |||||| ||||||||||||||||||
gtatcctttgattccttcatcatttgttttctttgttctttaatcatctggtttctgcttattactatggtacttgagctccagtggcataatattgtacctcttaactagacctccttagACCAACAAGGACATCACAGCACAAATCATCTCTGCTAGTATAGCAGGTGATATGGTTCTTGCTTCTGCTTACTCGCATGAGTTGCCACGATATGGTCTTG

upper sequence: GLYMA07G06590.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0094g00870.t01 (Vitis vinifera), 3'ss of exon 3
-tacttaatatttgtttattattttatttatgcctttggtatggcatatgaatgattaaatatgcttttcctgtgagtgt--aaaccttgacctatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG
 |   | |  ||| ||   | ||| | | |||   ||  | | |  | | |      ||  || || | |   |||   |  ||||||| ||||  ||||||||  |||||||| ||| |||| ||||||| ||| |||||||||||||| ||||| || |||||| | |||||| | |||||||| || |  ||||| ||||
ctgggttactttt-ttccctctttcaatgatgagctt--tgttgtttgttatctgccaagcattctgtgctgttgatctttgaaaccttaaccttgttactagACTAACAAGGATATTATTGCCCAAATAACATCCGCTAGCATTGCTGGTGATATAGTCCTTGCTTCTGCATATTCTCATGAGCTACCTCACTATGGACTTG

upper sequence: GLYMA07G06590.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0174g00190.t01 (Vitis vinifera), 3'ss of exon 4
tacttaatatttgtttattattttatttatgcctttggtatgg---catatgaatgattaaa---tatgcttttcctgtgagtgtaaaccttgacctatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG
      || ||| |||   || |  || | |   ||  | |||    | ||  |  || | |   | |  ||||||| |   |||||||||| ||    ||   |||  |||||||| ||   ||| ||||| ||||||||||| |||||||| ||||| |||||||| || || ||| | ||||| ||||| |  ||||| ||||
------atttttatttgacatatagttgaaggtcttattttgggggtaaatagacaatcatactgtttctttttcctctttttgtaaaccttaacactattctcagACGAACAAGGATATAACTGCTCAAATTATATCTGCTAGTATTGCTGGTGATATGGTTCTTGCAGCGGCCTATTCCCATGAACTGCCTCACTATGGGCTTG

upper sequence: GLYMA07G06590.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S364_3V6.1 (Physcomitrella patens), 3'ss of exon 3
tacttaatatttgtt-tattattttatttatgcctttggtatggcatatgaatga-ttaaatatgcttt---tcctgtgagtgtaaaccttgacctatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG
   |  | |||| || ||  ||    | | |    || ||   | ||||| ||   ||   ||  | |    |  | ||   ||| ||||||||   |||   ||| ||| |||||||||||||| ||||| |  | |||||   ||||||| |||||||| ||| || | |||||||| ||||||||||| || ||||| ||  
cgttggaaattttttctaagataagctctgtagggttagt---gtatatggatatcttctgtagacgtaggattttttgcaagtacaccttgactcgttt--cagACCAATAAGGACATTGTTGCCCAAATCACCTATGCTACTCTTGCTGGTGATATTGTGCTTACTTCCGCATATGCTCATGAGCTGCCTCGGTATGGACTCA

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|254340071|gb|GR858196.1|GR858196
EST:     AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT                         ---------GACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTTgtatcctttt ... tatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|9203772|gb|BE329996.1|BE329996
EST:     AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT                         AGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTTgtatcctttt ... tatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|37996752|gb|CF808341.1|CF808341
EST:     AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT                         AGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTTgtatcctttt ... tatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|10844117|gb|BF067454.1|BF067454
EST:     AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT                         AGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTTgtatcctttt ... tatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|8282719|gb|BE020280.1|BE020280
EST:     AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT                         AGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTTgtatcctttt ... tatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|10847099|gb|BF069865.1|BF069865
EST:     AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT                         AGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTTgtatcctttt ... tatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|10845936|gb|BF068951.1|BF068951
EST:     AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT                         AGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTTgtatcctttt ... tatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|15815279|gb|BI787554.1|BI787554
EST:     AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT                         AGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTTgtatcctttt ... tatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgaatgattaaatatgcttttcctgtgagtgtaaaccttgacctatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG
                                   aaccttgac  putative branch site 
                                           cctattt  CT-rich tract
        attaaatatgctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacttaatatttgtttattattttatttatgcctttggtatggcatatgaatgattaaatatgcttttcctgtgagtgtaaaccttgacctatttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - -tatgcct
- - - - - - - - - - - - - - - - - -tggtatg
- - - - - - - - - - - - - - - - - - - - - gcatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgagtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttgac