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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAAGACGAGAAAATTCTCTTATAGAGCCATATTTGGCAGCACATCATCAGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAGgtgcaggactgcacttattcatttctacacaaaactttctattttgcaagttggattacttttactttgttgcttctgccactcctccctattgtgtatt...

Basic information

species Glycine max
transcript GLYMA11G16220.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G16220.1 (Glycine max), 5'ss of exon 7
lower sequence: AT5G36890.1 (Arabidopsis thaliana), 5'ss of exon 7
AGGAAGACGAGAAAATTCTCTTATAGAGCCATATTTGGCAGCACATCATCAGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAGgtgcaggactgcacttattcatttctaca-caaaactttctattttgcaagttggattacttttactttgttgcttctgccactcctccctattgtgtatt-------------------------------------------------------------------------
 ||||||   || ||  |  | || || ||||||||||   ||||||||||| || ||||||||||| | ||||| ||||||||  | ||||| ||||||||   | |      |  |    |||  || |  || ||| | || |   | |||||    |     |  |  | |    | |    ||  |  |    ||                                                                          
TGGAAGAAATGAGAAGCCCTTGATCGAACCATATTTGGTCTCACATCATCAGGTTCTGGCCCATGCAACTGCTGTATCCATATATAGAAGCAAGTACAAGgtatggtagctttttattgtggttcagcaacctaattttgttttattttacttggacctttggctatcggaagatgtctcaaaggttctgttgttgacatctggtacctttatcaatgcatctcaattgcttgttatttaccagtgtgcgtttggtttacatatattaatctag

upper sequence: GLYMA11G16220.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv00s0220g00070.t01 (Vitis vinifera), 5'ss of exon 6
AGGAAGACGAGAAAATTCTCTTATAGAGCCATATTTGGCAGCACATCATCAGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAGgtgcaggactgcacttattcatttctacacaaaactttctattttgcaagttggattacttttactttgttgcttctgccactcctccctattgtgtatt---
 ||||| |  ||| ||||    | ||||||||||||||  |||||||| ||| | || |||||||| || ||||||||||||||| | | |||||| |||||          |  | |  |||  ||    || |  |  || || ||| |   | |  ||| | | | ||   | ||||| |      ||| ||| |     
TGGAAGGCAGGAACATTCATCAACAGAGCCATATTTGGTTGCACATCACCAGCTCTTAGCCCATGCTGCTGCTGTTTCCATATACAGAAACAAATATAAGgtatgctgtatgatgtctctattatta-gttaagcacttcatcttccaaatgaaaatggtttaaatgtatttagt-tgccatttggttttat-gtgaagcaca
















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|151395074|gb|EV264945.1|EV264945
EST:     AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAG                         -ATAAGCAAGGGG-ACAAGTGGGCTTTGTGGTAGATTGTGAATGGGC
genomic: AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAGgtgcaggact ... gacattccagGATAAGCAAGGGGGACAAGTGGGCTTTGTGGTAGATTGTGAATGGGC
EST: gi|192300022|gb|FG991840.1|FG991840
EST:     AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAGG                         GATAAGCAAGGGG-ACAAGTGGGCTTTGTGGTAGATTGTGAATGGGC
genomic: AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAGgtgcaggact ... gacattccagGATAAGCAAGGGGGACAAGTGGGCTTTGTGGTAGATTGTGAATGGGC
EST: gi|254323234|gb|GR840039.1|GR840039
EST:     AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAG                         GATAAGCAAGGGGGACAAGTGGGCTTTGTGGTAGATTGTGAATGGGCAGAG
genomic: AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAGgtgcaggact ... gacattccagGATAAGCAAGGGGGACAAGTGGGCTTTGTGGTAGATTGTGAATGGGCAGAG
EST: gi|192296626|gb|FG991194.1|FG991194
EST:     AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAG                         -ATAAGCAAGGGG-ACAAGTGGGCTTTGTGGTAGATTGTGAATGGGC
genomic: AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAGgtgcaggact ... gacattccagGATAAGCAAGGGGGACAAGTGGGCTTTGTGGTAGATTGTGAATGGGC
EST: gi|193540386|gb|FK497410.1|FK497410
EST:     AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAG                         GATAAGCAAGGGGGACAAGTGGGCTTTGTGGTAGATTGTGAATGGGCAGTG
genomic: AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAGgtgcaggact ... gacattccagGATAAGCAAGGGGGACAAGTGGGCTTTGTGGTAGATTGTGAATGGGCAGAG
EST: gi|26268409|gb|CA819472.1|CA819472
EST:     AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAG                         GATAAGCAAGGGGGACAAGTGGGCTTTGTGGTAGATTGTGAATGGGCAGAG
genomic: AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAGgtgcaggact ... gacattccagGATAAGCAAGGGGGACAAGTGGGCTTTGTGGTAGATTGTGAATGGGCAGAG
EST: gi|193414133|gb|FK376167.1|FK376167
EST:     AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAG                         GATAAGCAAGGGGGACAAGTGGGCTTTGTGGTAGATTGTGAATGGGCAGAG
genomic: AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAGgtgcaggact ... gacattccagGATAAGCAAGGGGGACAAGTGGGCTTTGTGGTAGATTGTGAATGGGCAGAG
EST: gi|20448999|gb|BQ253123.1|BQ253123
EST:     AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAG                         GATAAGCAAGGGGGACAAGTGGGCTTTGTGGTAGATTGTGAATGGGCAGAG
genomic: AGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAGgtgcaggact ... gacattccagGATAAGCAAGGGGGACAAGTGGGCTTTGTGGTAGATTGTGAATGGGCAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAAGACGAGAAAATTCTCTTATAGAGCCATATTTGGCAGCACATCATCAGATTTTGGCCCATGCAGCAGCTGTTTCCATATACCGGAGCAAATACAAGgtgcaggactgcacttattcatttctacacaaaactttctattttgcaagttggattacttttactttgttgcttctgccactcctccctattgtgtatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctcc