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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTGGCCTGTACGTACACCCAGGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAGgtaaactcagttgttaccaagtgtctcctccatgatctaattgtgatagccttcatgcttaatgacttctgttttttacag

Basic information

species Glycine max
transcript GLYMA07G00430.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 9
ACTTGGCCTGTACGTACACCCAGGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAGgtaaactcagttgttaccaagtgtctcctccatgatctaattgtgatagccttc---atgcttaatgacttctgttttttacag---------------------------------------------------------------
|| |||||||| ||| |||| |||||||||||||| || ||||| || ||||| |||||||| || || |||||      |   ||| ||  | |  |  |     ||  |||| | |  |  |||   |  ||| |      |     ||| |||                                                               
ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctataagttgccttgagcttggttgtcaat--aattatcaatgttttctaaaaacttgaaattgccaagcattttcagatgatgtttcacttcatcttactgaattaaccttaagtcttgtttgcttacaaatggttgcag

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 9
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 9
ACTTGGCCTGTACGTACACCCAGGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAGgtaa--actcagttgttaccaagtgtctcctccatgatctaattgtgatagccttcatgcttaatgacttctgttttttacag----
|  |||||||||||||| || ||||| ||||||||||| ||||| || ||||||||||| ||||| || ||||| |  ||||  ||  | |    |         ||  ||  |||   |||    |  |||| | ||  |||| |||  |   |    
AGCTGGCCTGTACGTACGCCTAGGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAGgtgattactcgattaattcttcttacagtggtgatagtc--atttgaatacatgtgttgctgattgctttct-tttcctgttgtcag

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 9
ACTTGGCCTGTACGTACACCCAGGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAGgtaaactcagttgttaccaagtgtctcctccatgatctaat-tgtgatagccttcatgcttaatg---acttctgttttttacag--------
|||||||||||||||||||| ||||||||||| ||||| || || |||||||| || || ||||| || |||||||      |    || || ||| |  ||  |  ||| || | ||   || |  | |||| | |     | ||| |||||            
ACTTGGCCTGTACGTACACCTAGGCCTGTTGCGTCAAAGCTGGCTGCTGATACCCCACTACTTACAGGACAGgtaattagcatacaaactaaatgtattatcagtattctcatctatggctgc-tgtaagcttgaagtgtgttcctgatttttgtttcatctcag

upper sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 9
ACTTGGCCTGTACGTACACCCAGGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAGgtaaactcagttgttaccaagtgtctcctccatgat---ctaattgtgatagccttcatgcttaatgacttctgttttttacag
||||||||||| |||||||| ||||||||||| ||||| ||||| |||||||| ||||| |||||||| |||||||       ||| |     |  | | | |||||    |   |||  || |   |      || |  ||| |||  | |||||
ACTTGGCCTGTCCGTACACCTAGGCCTGTTGCCTCAAAGCTTGCTGCTGATACACCTCTCCTTACTGGGCAGgtaatgcatcctgtcaaggtttagcccatacatgactaccattttgaaatgggtatttctgatactttcttttgtactctacag

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|120532286|gb|EH260419.1|EH260419
EST:     GGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAG                         CGTGTTCTTGATGCCCTTTTCCCCTC
genomic: GGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAGgtaaactcag ... ttttttacagCGTGTTCTTGATGCCCTTTTCCCCTC
EST: gi|192311315|gb|FK003450.1|FK003450
EST:     CTTCTTACTGGTCAG                         CGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATT
genomic: CTTCTTACTGGTCAGgtaaactcag ... ttttttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATT
EST: gi|192305155|gb|FG993935.1|FG993935
EST:     GGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCT-CT-ACTGGTCAG                         CGTGTTCTTGATGCCCTTT-CCCCT
genomic: GGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAGgtaaactcag ... ttttttacagCGTGTTCTTGATGCCCTTTTCCCCT
EST: gi|209728747|gb|BW655427.1|BW655427
EST:     GGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAG                         CGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATT
genomic: GGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAGgtaaactcag ... ttttttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATT
EST: gi|192311314|gb|FK003449.1|FK003449
EST:     CTTCTTACTGGTCAG                         CGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATT
genomic: CTTCTTACTGGTCAGgtaaactcag ... ttttttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTGGCCTGTACGTACACCCAGGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAGgtaaactcagttgttaccaagtgtctcctccatgatctaattgtgatagccttcatgcttaatgacttctgttttttacag

- - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC