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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggcaaatgttagtttggtagaatgttcattttgttagtagagaagatcaagattttaaatgaaagtgacataatgtaggcaagcatttgatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCCAAAGAATGGGA

Basic information

species Glycine max
transcript GLYMA06G12760.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G12760.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 1
-----taggcaaatgttagtttggtagaatgttcattttgttagtagagaagatcaagattttaaatgaaagtgacataatgtaggcaagcatttgatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCCAAAGAATGGGA
     |||       ||  | |  || || | |||| ||    | |    |  | || |     ||     |     |  |   |  |    |||| ||||||||||||||| || || || ||||| || || ||||| || |||||||| ||||||||||| || || ||||| |||||||||| ||| |   | |  |    
tgcagtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatata-gtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCT----

upper sequence: GLYMA06G12760.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g08830.1 (Oryza sativa), 3'ss of exon 1
-taggcaaatgttagtttggtagaatgttcattttgttagtagagaagatcaagattttaaatgaaagtgacataatgtaggcaagcatttgatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCCAAAGAATGGGA
 |||       ||  | |  || || | |||| ||    | |    |  | || |     ||     |     |  |   |  |    |||| ||||||||||||||| || || || ||||| || || ||||| || |||||||| ||||||||||| || || ||||| |||||||||| ||| |   | |  |||||
gtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatata-gtttgttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA

upper sequence: GLYMA06G12760.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G087590_T05 (Zea mays), 3'ss of exon 1
taggcaaatgttagtttggtagaatgttcattttgttagtagagaagatcaagattttaaatgaaagtgacataatgtaggcaagcatttgatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCCAAAGAATGGGA
         || || |        | ||  | || ||  |    |     |   | || |||     |  ||| |||  |      | | | ||||||||||||||| ||||| |||||||| || || ||||| || || || || ||||| ||||| || || || || |||||||||| ||| ||  | |  |    
---------gtgagctcttcttcttctttttcttctttctctgcagtgaaatactgttgaattgtttt--catgatgctgatcg--aatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCT----

upper sequence: GLYMA06G12760.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G087590_T01 (Zea mays), 3'ss of exon 1
taggcaaatgttagtttggtagaatgttcattttgttagtagagaagatcaagattttaaatgaaagtgacataatgtaggcaagcatttgatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCCAAAGAATGGGA
         || || |        | ||  | || ||  |    |     |   | || |||     |  ||| |||  |      | | | ||||||||||||||| ||||| |||||||| || || ||||| || || || || ||||| ||||| || || || || |||||||||| ||| ||  | |  |||||
---------gtgagctcttcttcttctttttcttctttctctgcagtgaaatactgttgaattgtttt--catgatgctgatcg--aatcgttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCTGGGA

upper sequence: GLYMA06G12760.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 1
taggcaaatgtt-agtttggtagaatgttcattttgttagtag-agaagatcaagattttaaatgaaagtgacataatgtag-gcaagcatt-tgatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCCAAAGAATGGGA
     |||| || ||  |  | | |  || ||| |   ||| | |  |   ||  ||  ||  ||  | |    |  ||||  | ||   |  || ||||||||||||||| || || || || || || |||||||| ||||| ||||||||||| |||||||||||||| || |||  |||    || ||  |||| ||| |
--cataaatctttaggct--ttggacattgattcttggagttgtattatgacagtatagtagttgggaatttgttggtgtaatgtaattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA

upper sequence: GLYMA06G12760.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g15360.t01 (Vitis vinifera), 3'ss of exon 1
--taggcaaatgttagtttggtagaatgttcattttgttagtagagaagatcaagattttaaatgaaagtgacataatg-taggcaagcatttgatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCCAAAGAATGGGA
   |  |  |  |||    | || |      | |  || | |        ||    || ||||   || || ||   || |  | ||  || || |||||||||||||||||| || || || |||||||| || |||||||| |||||||||||||||||||| |||||||| |||| |||   ||| ||    |  |||||
ttgaaacttaaattaacaagctaaagca---actgggtcacttagagctctctctgttgtaaagtgaactgtcaccttgattagtaaagatgtgctcagacagGTTGGAGGACATACCGGAGACCGGATGAAAAATCTGGAGGCCATGGTGTTGGATGGAGTCCGATTATTCCTTACATCTTTTCAGTCCCTTCTGGTTGGGA

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|8669138|gb|BE190245.1|BE190245
EST:     AGGCCTTCTAGCTGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         GTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTG
genomic: AGGCCTTCTAGCTGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcac ... gatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTG
EST: gi|120529314|gb|EH257448.1|EH257448
EST:     AGGCCTTCTAGCTGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         GTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTG
genomic: AGGCCTTCTAGCTGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcac ... gatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTG
EST: gi|213593009|gb|DB969863.1|DB969863
EST:     AGGCCTTCTAGCTGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         GTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTG
genomic: AGGCCTTCTAGCTGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcac ... gatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTG
EST: gi|15814233|gb|BI786508.1|BI786508
EST:     AGGCCTTCTAGCTGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         GTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTG
genomic: AGGCCTTCTAGCTGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcac ... gatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatcaagattttaaatgaaagtgacataatgtaggcaagcatttgatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCCAAAGAATGGGA
                                         atttgat  putative branch site (score: 5)
     aagattttaaatgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggcaaatgttagtttggtagaatgttcattttgttagtagagaagatcaagattttaaatgaaagtgacataatgtaggcaagcatttgatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCCAAAGAATGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagcat