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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTGCAGTGGGGATCTTAGCCCTCCAGAATATCATCATTATGGGCTTGCAGCTCTTTTGTATACCCATTTCACATCACCTATAAGAAGATATGCAGTAGgtatgccatattataataatatgtttgcttggtcaattgtgcacaatattgtgaagcgaaacttttttcccctgcag

Basic information

species Glycine max
transcript GLYMA04G39980.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39980.1 (Glycine max), 5'ss of exon 20
lower sequence: AT2G17510.2 (Arabidopsis thaliana), 5'ss of exon 21
---TTCTGCAGTGGGGATCTTAGCCCTCCAGAATATCATCATTATGGGCTTGCAGCTCTTTTGTATACCCATTTCACATCACCTATAAGAAGATATGCAGTAGgtatgccatattataataatatgtttgcttggtcaattgtgcacaatattgtgaagcgaaacttttttcccctgcag---
   ||||| ||||||||||| || ||||| |||||||||||||||||||||||||| |   ||||||| ||||| ||||| |||||  | ||||||||    |||| |  |||  |      | | ||  ||   |  |   ||     |  | | |    |  ||| ||||||  |      
TACTTCTGTAGTGGGGATCTCAGTCCTCCCGAATATCATCATTATGGGCTTGCAGCACCCCTGTATACTCATTTTACATCCCCTATCCGTAGATATGCC---Ggtaagtgata--actgctctgtcttccctcttttcacc-tgttagctgctctaatctta--cttctttccctggttctag

upper sequence: GLYMA04G39980.1 (Glycine max), 5'ss of exon 20
lower sequence: Vv07s0031g02190.t01 (Vitis vinifera), 5'ss of exon 20
---TTCTGCAGTGGGGATCTTAGCCCTCCAGAATATCATCATTATGGGCTTGCAGCTCTTTTGTATACCCATTTCACATCACCTATAAGAAGATATGCAG--TAGgtatgccatattataataatatgtttgcttggtcaattgtgca-caatattgtgaagcgaaact-tttttcccctgcag
   ||||| |||||||||||||| || |||||||  |||||||||||||||||||| | | | ||||| |||||||| || |||||||| ||||||||||  |||  |   | |  | |  |    ||||  |||||| ||| |   |   ||| | ||||  | ||||   |||    |||||
TACTTCTGTAGTGGGGATCTTAGTCCCCCAGAATTCCATCATTATGGGCTTGCAGCACCTCTCTATACTCATTTCACCTCTCCTATAAGGAGATATGCAGgttagtaagagcgttatctgttcg-gtgttcacttggtgaataggataattataatttgaattggaactaccttttttttgcag
















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|192304827|gb|FG997037.1|FG997037
EST:     AGCTCCTTTGTATACCCATTTCACATCACCTATAAGAAGATATGCAG-A-                         -TGTCATTGTGCACAGGCTACTTGCTGCTTCTTTAGGGATATCCAAGTTAC
genomic: AGCTCTTTTGTATACCCATTTCACATCACCTATAAGAAGATATGCAGTAGgtatgccata ... tcccctgcagATGTCATTGTGCACAGGCTACTTGCTGCTTCTTTAGGGATATCCAAGTTAC
EST: gi|51335336|gb|CO979202.1|CO979202
EST:     AGCTCCTTTGTATACCCATTTCACATCACCTATAAGAAGATATGC---AG                         ATGTCATTGTGCACAGGCTACTTGCTGCTTCTTTAGGGATATCCAAGTTAC
genomic: AGCTCTTTTGTATACCCATTTCACATCACCTATAAGAAGATATGCAGTAGgtatgccata ... tcccctgcagATGTCATTGTGCACAGGCTACTTGCTGCTTCTTTAGGGATATCCAAGTTAC
EST: gi|7232728|gb|AW568082.1|AW568082
EST:     AGCTCCTTTGTATACCCATTTCACATCACCTATAAGAAGATATGCAG-A-                         -TGTCATTGTGCACAGGCTACTTGCTGCTTCTTTAGGGATATCCAAGTTAC
genomic: AGCTCTTTTGTATACCCATTTCACATCACCTATAAGAAGATATGCAGTAGgtatgccata ... tcccctgcagATGTCATTGTGCACAGGCTACTTGCTGCTTCTTTAGGGATATCCAAGTTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTGCAGTGGGGATCTTAGCCCTCCAGAATATCATCATTATGGGCTTGCAGCTCTTTTGTATACCCATTTCACATCACCTATAAGAAGATATGCAGTAGgtatgccatattataataatatgtttgcttggtcaattgtgcacaatattgtgaagcgaaacttttttcccctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG