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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGGTTCCCTTCTCTCCTTTTTCCTATCTACATACACAACATACACAAAGCAAAGCATGGGAGTGACTCTGGAGTTTATGACACAGAAGGACGgtaagcgatgcaaattaatgaattaatgatcatgcattaaaaaaaatgtatcatgttactattgactatgatttgtcctttaatgaaatgaaaccacag

Basic information

species Glycine max
transcript GLYMA10G33350.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G33350.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv05s0049g01780.t01 (Vitis vinifera), 5'ss of exon 4
AATTGGTTCCCTTCTCTCCTTTTTCCTATCTACATACACAACATACACAAAGCAAAGCATGGGAGTGACTCTGGAGTTTATGACACAGAAGGACGgtaagcgatgcaaattaatgaattaatgatcatgcattaaaaaaaatgtatcatgttactattgactatgatttgtcctttaatgaaatgaaaccacag
   ||| |||||||||   || ||||||||||||||||||||||||||||| | ||||||||||||||||| |||  ||||||||| |||||| |||||||  |     |   || | ||  || |||| | || | | | |  |  |   | | ||  | | |    |    ||      |||  |    |||
GGGTGGATCCCTTCTCCTTTTCTTCCTATCTACATACACAACATACACAAATCCAAGCATGGGAGTGACTCCGGAACTTATGACACTGAAGGAAGgtaagcactat---tgggtgtagtatggaacatgtactatatatactcgaggagagttcaatctattgtacccttcttttcc----aattgacttgcag

upper sequence: GLYMA10G33350.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S77_124V6.1 (Physcomitrella patens), 5'ss of exon 4
AATTGGTTCCCTTCTCTCCTTTTTCCTATCTACATACACAACATACACAAAGCAAAGCATGGGAGTGACTCTGGAGTTTATGACACAGAAGGACGgtaagcg-------atgcaaattaatgaattaatga---tcatgcattaaaaaaaatgtatcat-gttactattgactatgatttgtcctttaatgaaa--tgaaaccacag----------
  |||| |||| || |||||||| || ||||||||  | || || |||||||| ||||||||||||||||||| ||| ||||||||||| ||  ||||| |         |  || ||  ||     ||||   |||    | || ||  ||  ||  | |    |       ||||||      | |  | |   ||||||   |           
TCTTGGATCCCGTCGCTCCTTTTCCCAATCTACATCAAAAATATTCACAAAGCCAAGCATGGGAGTGACTCTGAAGTGTATGACACAGAGGGCAGgtaaacatcagttagtcaaactttgtgtgcccatgacggtcacagctgaagaaggattgattgtagggggtgaaagtcatgattgagtagtaatcggatcttgaaactggatgtgcttttag
















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|298195729|gb|HO044120.1|HO044120
EST:     ACAAAGCAAAGCATGGGAGTGACTCCTGGGGTTTATGACACAGAAGGACG                         TTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
genomic: ACAAAGCAAAGCATGGGAGTGACTC-TGGAGTTTATGACACAGAAGGACGgtaagcgatg ... gaaaccacagTTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
EST: gi|298185669|gb|HO030882.1|HO030882
EST:     ACAAAGCAAAGCATGGGAGTGACTCCTGGAGTTTATGACACAGAAGGACG                         TTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
genomic: ACAAAGCAAAGCATGGGAGTGACTC-TGGAGTTTATGACACAGAAGGACGgtaagcgatg ... gaaaccacagTTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
EST: gi|213591840|gb|DB973405.1|DB973405
EST:     CACAAAGCAAAGCATGGGAGTGACTCTGGAGTTTATGACACAGAAGGACG                         TTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
genomic: CACAAAGCAAAGCATGGGAGTGACTCTGGAGTTTATGACACAGAAGGACGgtaagcgatg ... gaaaccacagTTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
EST: gi|298192764|gb|HO033198.1|HO033198
EST:     ACAAAGCAAAGCATGGGAGTGACTCCTGGAGTTTATGACACAGAAGGACG                         TTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
genomic: ACAAAGCAAAGCATGGGAGTGACTC-TGGAGTTTATGACACAGAAGGACGgtaagcgatg ... gaaaccacagTTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
EST: gi|298184162|gb|HO029375.1|HO029375
EST:     CACAAAGCAAAGCATGGGAGTGACTCTGGAGTTTATGACACAGAAGGACG                         TTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
genomic: CACAAAGCAAAGCATGGGAGTGACTCTGGAGTTTATGACACAGAAGGACGgtaagcgatg ... gaaaccacagTTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
EST: gi|298179629|gb|HO024844.1|HO024844
EST:     CACAAAGCAAAGCATGGGAGTGACTCTGGAGTTTATGACACAGAAGGACG                         TTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
genomic: CACAAAGCAAAGCATGGGAGTGACTCTGGAGTTTATGACACAGAAGGACGgtaagcgatg ... gaaaccacagTTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
EST: gi|298164832|gb|HO010829.1|HO010829
EST:     ACAAAGCAAAGCATGGGAGTGACTCCTGGAGTTTATGACACAGAAGGACG                         CTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
genomic: ACAAAGCAAAGCATGGGAGTGACTC-TGGAGTTTATGACACAGAAGGACGgtaagcgatg ... gaaaccacagTTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
EST: gi|298182340|gb|HO026515.1|HO026515
EST:     CACAAAGCAAAGCATGGGAGTGACTCTGGAGTTTATGACACAGAAGGACG                         TTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT
genomic: CACAAAGCAAAGCATGGGAGTGACTCTGGAGTTTATGACACAGAAGGACGgtaagcgatg ... gaaaccacagTTATGTGCCAGCAAATATTGAGAACATATTCAGTAAGTATGCTCGTACAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGGTTCCCTTCTCTCCTTTTTCCTATCTACATACACAACATACACAAAGCAAAGCATGGGAGTGACTCTGGAGTTTATGACACAGAAGGACGgtaagcgatgcaaattaatgaattaatgatcatgcattaaaaaaaatgtatcatgttactattgactatgatttgtcctttaatgaaatgaaaccacag

- - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG