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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttccttctaccattcagaatacataatatacagtgacagtaacaggacaaccatattccatcactgaaccgaacgtccattattaaataagtaaaacttgaataaatattgatgaagtacaggccttaatccggtgcttaatgatccatccttattgaaaattgcagGAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACATGATTACCATGTGGGTTGCATAAGAAAGTGGTTGTCTATGAAGAAAGTTT

Basic information

species Glycine max
transcript GLYMA13G20210.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20210.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0040g02160.t01 (Vitis vinifera), 3'ss of exon 5
gtatgcttccttctaccattcagaatacataatatacagtgacagtaacaggacaaccatattccatcactgaaccgaacgtccattattaaataagtaaaacttgaataaatattgatgaagtacaggccttaatccggtgcttaatgatccatccttattgaaaattg-cagGAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACATGATTACCATGTGGGTTGCATAAGAAAGTGGTTGTCTATGAAGAAAGTTT
                                                                    ||  |  | |  ||     ||    ||  |   | | ||| || || | |  ||    |  |  |||   |||| |   |||   | |  ||||  |  ||| ||||| || |||||||||||||| ||||||||||| ||||  || ||  | ||||||||||||||||  ||||| |  || ||||| |  ||||||||    |
------------------------------------------------------------------ctacgaattcaactgtttgggatatgctaccttgcattagaa-aattaataa--aaactgaaccactaacttggtggt--gtga---acctgtatttgattttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCATGATTACCATGTGGACTGCATCAAGAAATGGTTATTGATGAAGAACTCAT
















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|5510277|gb|AI856661.1|AI856661
EST:     ACTGTTCATCTGAGCAAAGTCAAGAAGAAGAAACTTGTGCAATCTGTCTG                         GAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACAT
genomic: ACTGTTCATCTGAGCAAAGTCAAGAAGAAGAAACTTGTGCAATCTGTCTGgtatgcttcc ... aaaattgcagGAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACAT
EST: gi|209720200|gb|BW674538.1|BW674538
EST:     ACTGTTCATCTGAGCAAAGTCAAGAAGAAGAAACTTGTGCAATCTGTCTG                         GAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACAT
genomic: ACTGTTCATCTGAGCAAAGTCAAGAAGAAGAAACTTGTGCAATCTGTCTGgtatgcttcc ... aaaattgcagGAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACAT
EST: gi|209701647|gb|BW673133.1|BW673133
EST:     ACTGTTCATCTGAGCAAAGTCAAGAAGAAGAAACTTGTGCAATCTGTCTG                         GAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACAT
genomic: ACTGTTCATCTGAGCAAAGTCAAGAAGAAGAAACTTGTGCAATCTGTCTGgtatgcttcc ... aaaattgcagGAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACAT
EST: gi|213616823|gb|DB977022.1|DB977022
EST:     ACTGTTCATCTGAGCAAAGTCAAGAAGAAGAAACTTGTGCAATCTGTCTG                         GAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACAT
genomic: ACTGTTCATCTGAGCAAAGTCAAGAAGAAGAAACTTGTGCAATCTGTCTGgtatgcttcc ... aaaattgcagGAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACAT
EST: gi|5761343|gb|AI966702.1|AI966702
EST:     ACTGTTCATCTGAGCAAAGTCAAGAAGAAGAAACTTGTGCAATCTGTCTG                         GAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACAT
genomic: ACTGTTCATCTGAGCAAAGTCAAGAAGAAGAAACTTGTGCAATCTGTCTGgtatgcttcc ... aaaattgcagGAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACAT
EST: gi|58016048|gb|CX702790.1|CX702790
EST:     ACTGTTCATCTGAGCAAAGTCAAGAAGAAGAAACTTGTGCAATCCGTCTG                         GAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACAT
genomic: ACTGTTCATCTGAGCAAAGTCAAGAAGAAGAAACTTGTGCAATCTGTCTGgtatgcttcc ... aaaattgcagGAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagtacaggccttaatccggtgcttaatgatccatccttattgaaaattgcagGAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACATGATTACCATGTGGGTTGCATAAGAAAGTGGTTGTCTATGAAGAAAGTTT
                       gcttaat  putative branch site (score: 4)
                                       ttattgaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttccttctaccattcagaatacataatatacagtgacagtaacaggacaaccatattccatcactgaaccgaacgtccattattaaataagtaaaacttgaataaatattgatgaagtacaggccttaatccggtgcttaatgatccatccttattgaaaattgcagGAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACATGATTACCATGTGGGTTGCATAAGAAAGTGGTTGTCTATGAAGAAAGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA