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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGACCCATGTACAGTAACCCACCTCTCCATGGAGCACTTATAGTTTCTACTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAGgtaaagtgccattatttcttagagtcccctcctccctctccctgggttttcaatgtagaagtagtgattttgatcatcacatacaataaacgaaccaaac...

Basic information

species Glycine max
transcript GLYMA06G42830.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G42830.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G146677_T01 (Zea mays), 5'ss of exon 7
TAGACCCATGTACAGTAACCCACCTCTCCATGGAGCACTTATAGTTTCTACTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAGgtaaagtgc--------cattatttcttagagtcccctcctccct------ctccctgggttttcaatgtagaagtagtgattttgatcatcacatacaataaacgaaccaaac
 ||||| |||||||| ||||||||| | ||||| |||||  | |||||||   ||||  |||||||||| |||||||  || ||| | |||||||||||||||||  |         ||| | | ||||  || |     |  ||       |   |   || | | || | ||  |  || | || ||| |||    | | |  |   ||   
AAGACCAATGTACAGCAACCCACCTGTTCATGGTGCACTGGTTGTTTCTATAATCCTCAGTGATCCAGAATTGAAGAGTTTGTGGTTAAAAGAAGTCAAGgtaaatcgtgaatcctacataagtacttaatgttcttatatggctaggtggttaaatctattgttagtgaataaagaaagaatgtggtcaacacgc-tattgattgtttcag--

upper sequence: GLYMA06G42830.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv12s0028g01820.t01 (Vitis vinifera), 5'ss of exon 7
TAGACCCATGTACAGTAACCCACCTCTCCATGGAGCACTTATAGTTTCTACTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAGgtaaagtgccattatttcttagagtcccctcctccctctccctgggttttcaatgtagaagtagtgattttgatcatcacatacaataaacgaaccaaac-
|||||||||||||||||| |||||| | || || || || || || || ||| | |||||||||||||| |||||||| |||||||| || ||||| |||||||  | | |||  |   |    ||     ||   | | | |   | |   ||     | || |  |||| |  |     ||||  ||   |      | 
TAGACCCATGTACAGTAATCCACCTGTTCAAGGTGCTCTCATTGTGTCAACTATTCTTGGTGATCCAGAATTGAAGAAATTATGGCTCAAGGAAGTTAAGgtaatttactattcctgtgttctttcttgaactttatttacgtccttgtcagataggcgaatactacttttcag-actttgtacatcaatttatgttggcg
















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|254345073|gb|GR851449.1|GR851449
EST:     CAGATTTGAAGAAGTTATGCCTTAAAGAAGTCAAG                         GTTATGGCAGA-CGCATCATCGGAATGAGGACTACACTACGAG-AAACTTA
genomic: CAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAGgtaaagtgcc ... atctttacagGTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACTTA
EST: gi|22523470|gb|BU082281.1|BU082281
EST:     CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAG                         GTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACCTA
genomic: CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAGgtaaagtgcc ... atctttacagGTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACTTA
EST: gi|254340272|gb|GR858397.1|GR858397
EST:     CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAG                         GTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACTTA
genomic: CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAGgtaaagtgcc ... atctttacagGTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACTTA
EST: gi|57574406|gb|CX547381.1|CX547381
EST:     CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAG                         GTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACTTA
genomic: CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAGgtaaagtgcc ... atctttacagGTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACTTA
EST: gi|254320419|gb|GR826868.1|GR826868
EST:     CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAG                         GTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACTTA
genomic: CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAGgtaaagtgcc ... atctttacagGTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACTTA
EST: gi|57574152|gb|CX547127.1|CX547127
EST:     CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAG                         GTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACTTA
genomic: CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAGgtaaagtgcc ... atctttacagGTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACTTA
EST: gi|254340271|gb|GR858396.1|GR858396
EST:     CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAG                         GTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACTTA
genomic: CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAGgtaaagtgcc ... atctttacagGTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACTTA
EST: gi|22523639|gb|BU082450.1|BU082450
EST:     CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAG                         GTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACCTA
genomic: CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAGgtaaagtgcc ... atctttacagGTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACTTA
EST: gi|14999882|gb|BI320696.1|BI320696
EST:     CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAG                         GTTATTGCAGACCGCATCATCAGAATGAGGACTACACTACGAGAAAACTTA
genomic: CTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAGgtaaagtgcc ... atctttacagGTTATGGCAGACCGCATCATCGGAATGAGGACTACACTACGAGAAAACTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGACCCATGTACAGTAACCCACCTCTCCATGGAGCACTTATAGTTTCTACTGTCCTTGGTGATCCAGATTTGAAGAAGTTATGGCTTAAAGAAGTCAAGgtaaagtgccattatttcttagagtcccctcctccctctccctgggttttcaatgtagaagtagtgattttgatcatcacatacaataaacgaaccaaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccctc