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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGCATGACTTGCGCATGATTCATACTGACCTGAAGCCTGAAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttctttttgcctacctgcgattatttgttgttttggaattgcactatacataatacgaagagcagttcctggttgataggggagttattaggaa...

Basic information

species Glycine max
transcript GLYMA17G13440.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13440.1 (Glycine max), 5'ss of exon 6
lower sequence: AT4G24740.1 (Arabidopsis thaliana), 5'ss of exon 7
TCATGCATGACTTGCGCATGATTCATACTGACCTGAAGCCTGAAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttctttttgcctacctgcgattatttgttgttttggaattgc--actatacataatacgaagagcagttcctggttgataggggagttattaggaa
| |||||||||||||||||||||||||| ||||| || || ||||| || ||  |||| ||  |||| ||||| ||  |||| || |||||||||  | ||            ||| | | | |||    ||    | ||  |||||  | | | |  |  | | ||  | ||   |   |  |          
TTATGCATGACTTGCGCATGATTCATACGGACCTTAAACCAGAAAATATTCTGTTAGTCTCCTCAGACTATGTGAAGATTCCCGAGTACAAGgtatatctc---------gaatgcaactgtgtgtgaccttaatgtggccaactattta-agtgctgaaggaatttggttgtgtttcctgatgcag-------

upper sequence: GLYMA17G13440.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 7
TCATGCATGACTTGCGCATGATTCATACTGACCTGAAGCCTGAAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttctttttgcctacctgcg-attatttgttgttttggaattgc---actatacataatacgaagagcagttcctggttgataggggagttattaggaa---------
| |||||||| || ||| | || ||||| ||  |||||||||| || ||||| ||||| || ||||| ||||| |||||||| ||||||||||||||     | ||  ||   || | ||||  ||   | | ||  ||||   | ||| | |  | |    |  |   ||| |||  |     |  |||| |            
TTATGCATGATTTACGCCTCATACATACGGATTTGAAGCCTGAGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAGgtactccagatgttaacttgatgtgtattaagtggcatat-ggttttgctttattattctttctgcatctacaatgcccttgttattgtaacatatatttgttgcattttcag
















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|21256128|gb|BQ453016.1|BQ453016
EST:     CTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: CTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|12772886|gb|BG237813.1|BG237813
EST:     AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|208219792|gb|GE018916.1|GE018916
EST:     AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|23728320|gb|BU762211.1|BU762211
EST:     AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|13481209|gb|BG510552.1|BG510552
EST:     AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|193479143|gb|FK444614.1|FK444614
EST:     TGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: TGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|193509579|gb|FK468373.1|FK468373
EST:     AAAACATACTAATAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCACCAAGTTCCTATT-CAAGAGAGTTCCCAAATCAAGT
genomic: AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|17518814|gb|BM187856.1|BM187856
EST:     AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|207790919|gb|GD760488.1|GD760488
EST:     TGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: TGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|19347043|gb|BM891931.1|BM891931
EST:     AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|193315306|gb|FK278908.1|FK278908
EST:     AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAAGAATAACACCAAGTTCCTATTTC
genomic: AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTA-GA-T--CACCAAGTTCCTATTTC
EST: gi|23728843|gb|BU762488.1|BU762488
EST:     AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|9986568|gb|BE660676.1|BE660676
EST:     AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTNCTGACTACCAG                         AGTTCATCTAGATCACC
genomic: AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACC
EST: gi|207758237|gb|GD730173.1|GD730173
EST:     TAGTTTCACCGGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAAATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: TAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|193594938|gb|FK546797.1|FK546797
EST:     AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|51334885|gb|CO978751.1|CO978751
EST:     AAAACATACTACTANNNTCACCAGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: AAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|193348366|gb|FK314348.1|FK314348
EST:     TCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: TCAAAGTTCCTGACTACAAGgtacttttct ... atttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGCATGACTTGCGCATGATTCATACTGACCTGAAGCCTGAAAACATACTACTAGTTTCACCAGAGTATGTCAAAGTTCCTGACTACAAGgtacttttctttttgcctacctgcgattatttgttgttttggaattgcactatacataatacgaagagcagttcctggttgataggggagttattaggaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggagt