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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGGAGAAATTTGTGTAAAGGGAAAAACCTTGTTTGCAGGGTACTACAAACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcatttatgttttccaaaattgaggtttatattcttatattagctgttgggttgggtcacaattttccttttattcacaaatgatatattcaacag

Basic information

species Glycine max
transcript GLYMA01G43470.2
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43470.2 (Glycine max), 5'ss of exon 15
lower sequence: LOC_Os01g46750.1 (Oryza sativa), 5'ss of exon 15
AGAGGAGAAATTTGTGTAAAGGGAAAAACCTTGTTTGCAGGGTACTACAAACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcatttatgttttccaaaattgaggtttatattcttatattagctgttgggttgggtcacaattttccttttattcacaa--atgatatattcaacag-
 | || ||||| ||  | | |||| ||||  | ||  |||| |||||||| ||||||||||| || || || ||| ||||||||| |||||||||||| ||| || ||  ||   |||||  |  ||    ||| | | |||||    ||| || |  | | |   | |         | | | ||  |||  | || | |    
CGTGGCGAAATCTGCATCAGGGGAGAAACAGTATTCTCAGGATACTACAAGCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTGgt-atgtc--ttgctttttcatagttttttttttctctccttatgggggctttttg--tagattttagtggctgcagcagtaaaaagaatgtcagataccatttc

upper sequence: GLYMA01G43470.2 (Glycine max), 5'ss of exon 15
lower sequence: GRMZM5G861300_T01 (Zea mays), 5'ss of exon 15
AGAGGAGAAATTTGTGTAAAGGGAAAAACCTTGTTTGCAGGGTACTACAAACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcatttatgttttccaaaattgaggtttatattcttat-attagctgttgggt---tgggtcacaattttccttttattcacaaatgatatattc-aacag-------------------------------------------------------------------------
 | ||||| || ||  | | |||| |||| || ||  |||| |||||||| ||||||||||| || || ||||| || ||||||| ||||||||| || |||  | |  |    ||| | |     ||   |||| ||  | || | ||    |        | | |   | ||    ||  ||  | ||||      ||| ||                                                                            
CGTGGAGAGATATGCATCAGGGGAGAAACATTATTCTCAGGATACTACAAGCGTGAAGACCTTACAAAGGAGGTCCTCATTGATGGATGGTTCCACACTGgtagtgtgttgcccgttctactgctctgtt-tttacatagtgatcactattcatgacacacattgttagtagttaaaattccatgtagaaatccagggttccaatcatataccatgaccaaaatttcctattttgtgctcccgcctataaaacctgacacatctgcctcatctgttgcag

upper sequence: GLYMA01G43470.2 (Glycine max), 5'ss of exon 15
lower sequence: AT4G11030.1 (Arabidopsis thaliana), 5'ss of exon 15
AGAGGAGAAATTTGTGTAAAGGGAAAAACCTTGTTTGCAGGGTACTACAAACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcatttatgttttccaaaattgaggtttatattcttatat-tagc-tgttgggt-tgggtcacaattttccttttattcacaaatgatatat---tcaacag
 |||| ||||| ||  ||   |||||||| || ||| |||||||||||||||||||||||||||| ||||||||| | || || | |||||| || |||||||| |  |    |     |    ||     |||   ||| ||||| |||| | ||   | |  ||    |||| |||| | |     ||  || | |   | | |||
CGAGGCGAAATATGCATACGAGGAAAAACTTTATTTTCAGGGTACTACAAACGTGAAGACCTCACAAAAGAGGTTTTTATCGACGGATGGTTGCACACAGgttactaaaaacctcaacactttgatcat--tttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatcttaccag

upper sequence: GLYMA01G43470.2 (Glycine max), 5'ss of exon 15
lower sequence: AT4G23850.1 (Arabidopsis thaliana), 5'ss of exon 15
AGAGGAGAAATTTGTGTAAAGGGAAAAACCTTGTTTGCAGGGTACTACAAACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcatttatg---ttttccaaaattgaggtttatattcttatattagctgttgggttgggtcacaattttccttttattc-acaaatgatatattcaacag
 | || ||||| ||  |   |||||| ||| | ||  | || ||||||||||||||||| ||||| ||||||||||| ||||||| |||| | || ||||||  ||   | | ||   || |  | ||||   |||   ||  |  | || |  ||  |||  | ||       | ||   | ||  |   | |||   |||    
CGTGGTGAAATCTGCATTCGGGGAAAGACCCTTTTCTCTGGTTACTACAAACGTGAAGATCTCACGAAAGAGGTTCTCATTGATGGATGGCTGCACACAGgtatttctttctctgaacttgtatacaatt--agttagaatattggtttttgtagtccggtgagttcttttcagttctcacactctgcttcttatactctcag---

upper sequence: GLYMA01G43470.2 (Glycine max), 5'ss of exon 15
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 15
AGAGGAGAAATTTGTGTAAAGGGAAAAACCTTGTTTGCAGGGTACTACAAACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcattt----atgttttccaaaattgaggtttatattcttatattagctgttgggttgggtcacaattttccttttattcacaaatgatatattcaacag
 | |||||||| ||  ||   || |||||||||||  | || ||||| ||||||||||| ||||| ||||||||  || |||||| ||||||||| |||||||   |||| |    || | |||   |||| || |||    || | ||||   ||| |  | |  ||   |    ||||    | |  | | || | |||| |||
CGTGGAGAAATATGCATACGAGGGAAAACCTTGTTCTCGGGATACTATAAACGTGAAGATCTCACCAAAGAGGTCTTGGTTGATGGATGGTTCCACACAGgtttgctcatattggcatttcttcttgaattaagttttgaggtcctctatt--ttgtggattcgtttctttaacaacctt--gctgatgacttatcttttca-cag

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|21676990|gb|BQ629341.1|BQ629341
EST:     ACGTGAAGACCTCACTAAAGAGTTTCTGATTGATGAATGGTTCCATACAG                         GGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
genomic: ACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcat ... tattcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
EST: gi|208127888|gb|GD924920.1|GD924920
EST:     GATGAATGGTTCCATACAG                         GGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGA
genomic: GATGAATGGTTCCATACAGgttatttcat ... tattcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
EST: gi|254347181|gb|GR856851.1|GR856851
EST:     ACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAG                         GGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
genomic: ACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcat ... tattcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
EST: gi|151396024|gb|EV265901.1|EV265901
EST:     ACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAG                         GGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
genomic: ACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcat ... tattcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
EST: gi|22525607|gb|BU084418.1|BU084418
EST:     ACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAG                         GGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
genomic: ACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcat ... tattcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
EST: gi|19270925|gb|BM887181.1|BM887181
EST:     GGTTCCATACAG                         GGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
genomic: GGTTCCATACAGgttatttcat ... tattcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
EST: gi|51342594|gb|CO983564.1|CO983564
EST:     ANNTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAG                         GGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
genomic: ACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcat ... tattcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
EST: gi|192295718|gb|FG990572.1|FG990572
EST:     ACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAG                         GGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
genomic: ACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcat ... tattcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
EST: gi|120533313|gb|EH261446.1|EH261446
EST:     ACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAG                         GGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
genomic: ACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcat ... tattcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
EST: gi|22525677|gb|BU084488.1|BU084488
EST:     ACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAG                         GGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA
genomic: ACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcat ... tattcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGGAGAAATTTGTGTAAAGGGAAAAACCTTGTTTGCAGGGTACTACAAACGTGAAGACCTCACTAAAGAGGTTCTGATTGATGAATGGTTCCATACAGgttatttcatttatgttttccaaaattgaggtttatattcttatattagctgttgggttgggtcacaattttccttttattcacaaatgatatattcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG