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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actagcatggcactaaggagcatctctttagaagggcttgccttgcagtgtttaaaactttaactgggtctcagtactgactgatgtttttgtatttcagGTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTAGTTCTCACAATGGAAGAATCCCTTGTTAACTTTCTTCAGGATGATGACA

Basic information

species Glycine max
transcript GLYMA10G31320.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G31320.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g00170.t01 (Vitis vinifera), 3'ss of exon 1
--actagcatggcactaaggagcatctctttag--aagggcttgccttgcagtgtttaaaactttaactgggtctcagtactgactgatgtttttgtatttcagGTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTAGTTCTCACAATGGAAGAATCCCTTGTTAACTTTCTTCAGGATGATGACA
    | | ||| || | |  ||    | ||| |  ||   |||    ||      ||  ||  ||   |   ||| |      |   || | ||     |||||||||||||||||||||||||| | |||||||||||||||||||||||||| |||||| |||| |||||| || | || ||||| ||||| || ||| |||
ttgtttg-atgtcatttataagtggtttttttgctaacatcttttgatgtttctcttgtaatcttcttt---tcttatattaaatcaatatcttcaacattcagGTTGAGGAATTGGCTTTTCTTATTAAGGACAATCTTCCTTGCAAGCATCTTGTTCTCTCAATTGAAGAAGCCTTGGTCAACTTCCTTCAAGACGATAACA
















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|11411987|gb|BF423998.1|BF423998
EST:     CCTTTGACTTTGTTCAATCCTTCGACATGAGTATGACCCAATTCGCCATG                         GTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTA
genomic: CCTTTGACTTTGTTCAATCCTTCGACATGAGTATGACCCAATTCGCCATGgtatgcttct ... tgtatttcagGTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTA
EST: gi|298188529|gb|HO035222.1|HO035222
EST:     CCTTTGACTTTGTTCAATCCTTCGACATGAGTATGACCCAATTCGCCATG                         GTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTA
genomic: CCTTTGACTTTGTTCAATCCTTCGACATGAGTATGACCCAATTCGCCATGgtatgcttct ... tgtatttcagGTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTA
EST: gi|298177235|gb|HO023482.1|HO023482
EST:     CCTTTGACTTTGTTCAATCCTTCGACATGAGTATGACCCAATTCGCCATG                         GTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTA
genomic: CCTTTGACTTTGTTCAATCCTTCGACATGAGTATGACCCAATTCGCCATGgtatgcttct ... tgtatttcagGTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTA
EST: gi|193637686|gb|FK583099.1|FK583099
EST:     CCTTTGACTTTGTTCAATCCTTCGACATGAGTATGACCCAATCCGCCATG                         GTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTA
genomic: CCTTTGACTTTGTTCAATCCTTCGACATGAGTATGACCCAATTCGCCATGgtatgcttct ... tgtatttcagGTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTA
EST: gi|27809203|gb|CB063625.1|CB063625
EST:     CCTTTGACTTTGTTCAATCCTTCGACATGAGTATGACCCAATTCGCCATG                         GTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTA
genomic: CCTTTGACTTTGTTCAATCCTTCGACATGAGTATGACCCAATTCGCCATGgtatgcttct ... tgtatttcagGTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTA
EST: gi|193650376|gb|FK597221.1|FK597221
EST:     AATCCTTCGACATGAGTATGACCCAATTCGCCATG                         GTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTA
genomic: AATCCTTCGACATGAGTATGACCCAATTCGCCATGgtatgcttct ... tgtatttcagGTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgtttaaaactttaactgggtctcagtactgactgatgtttttgtatttcagGTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTAGTTCTCACAATGGAAGAATCCCTTGTTAACTTTCTTCAGGATGATGACA
                                       tgttttt  CT-rich tract
     tttaaaactttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actagcatggcactaaggagcatctctttagaagggcttgccttgcagtgtttaaaactttaactgggtctcagtactgactgatgtttttgtatttcagGTTGAGGAATTGGCTTTTCTTGTCAAGGACAATCTTCCTTGCAAGCATCTAGTTCTCACAATGGAAGAATCCCTTGTTAACTTTCTTCAGGATGATGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - gcatggc
- - - - - - - - - - - - - - - - - - - - ccttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtt