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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttatttgagtttaccttgcttgctattaggattttatctggcacttcatcctatggttttgtcatgataaaactaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG

Basic information

species Glycine max
transcript GLYMA20G33910.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 13
gtttgtttatttgagtttaccttgcttgctattaggattttatctggcacttcatcctatggttttgtcatgataaaactaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG
        | |   ||| |   ||   | |   |      |    ||        |||   ||| | |  |||      ||         ||||   |  | ||||| |||||||||||||| |||||||||||||||||||||||||||||||||||||| || ||||| || || || ||||| || ||||| || ||||| |
--acacacaatgatgttgagaatggaagttga-attgcactgctaggagtggtgccctgaagttatattttgacctgtatatgcatcatgacctt--tcctacagATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAG

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 13
---gtttgtttatttgagtttaccttgcttgctattaggattttatctggcacttcatcctatggttttgtcatgataaaactaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG
   |   |   |||  |  ||||  |   || |  |||    |   |||     | | | |  ||| || |  |  |  ||  || |  || | | |  ||||   ||||||| ||||| ||||| || || |||||||||||||||||||||||||| |||||  ||||||| ||||| || |||||||||||||| || ||||| |
agtggcggaacattcta--ttactattactgattctagtgactgtcctgagttgtgagcatg-ggtattatttttttttaa--aaaaattggatctttccttt---agATTGGTGGAGCTAGTGAAGCGGAGGTTGGTGAGAAGAAGGATAGAGTGACTGATGCACTAAATGCTACCAAAGCTGCTGTAGAGGAGGGTATTGTACCAG

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 12
-------------------------gtttgtttatttgagtttac-----cttgcttgctattaggattttatctggcacttcatcctatggttttgtcatgata---aaactaacatctgaaacctca--cttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG
                          |||    ||   || ||||     |||| ||  |||    ||| ||      |||    ||| ||| | | | ||  |     |  |     ||       ||  ||||   |||||||||||||||| || || |||||||||||||||||||||||||||||||||||  | ||||| || || || ||||| || |||||||| ||||| |
gtgaggttattgacctactgtatgtatttacgaatggtagattacatgttcttgttttatatcgtaattgtaata---actgttacctgtggctctctgatatttcctgattttgtgcctatgtgtgcatcctttcctagATTGGAGGAGCCAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGCATTGTACCAG

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
----------------------gtttgtttatttgagtttaccttgctt--gctattaggattttatc-tggcacttcatcctatg---gttttgtcatgataaaactaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG
                      ||||  | ||   || || || || ||     |||    || | |  |   |||    ||| ||   ||  |    |     |  |     |||   |||| ||||   ||||||| ||||| || || || |||||||||||||||||||||||||||||||||||  | ||||| || || || ||||| || ||||| || ||||| |
gtgagattactgacctttgtatgtttactaatggcagatt-ccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtg-cctc-ctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 13
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
gtttgtttatttgagtttaccttgcttgctattaggattttatctggcacttcatcctatggttttgtcatgataaaactaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG
             | | |||    ||||  |  |  |   ||   |||  || || |  |  |  | |  |  |||     | ||     |  |   ||||  ||||||||||||| |||||| | |||||| |||| ||||| |||||||| || |||||  ||||||| || || ||||| ||||||||||| || || || |
-----------gtaatgtacacctcttgtgaacatcagactaataggctattaatgcattattagtttattactaatgtcgagattactcatatgggtttt-tagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
gtttgtttatttgagtttaccttgcttgctattaggattttatctggcacttcatcctatggttttgtcatgataaaactaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG
||| ||  || | |   |   |||   | | |||| ||  || | |   | |  |  || |    |||| || || ||||    |||| | |      | |  ||||||||||||| ||||| |||||||||||||||||||| || |||||||||||||| || ||||| || || ||||| || || ||||| ||  |||| |
gttagtccatgttataatgttttgggag-tcttagaatcatagcag---cctggttgtaag----tgtcttgttataact----tctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
--------------------------gtttgtttatttga--gtttaccttgcttgc-tattaggattttatctg--gcacttcatcctatggttttgtcatgataaa-actaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG
                          |||   |  |||||   |  |  ||  | ||  | ||  ||  |  |||  ||| ||||  |  |    ||   ||  |||    |   || |    | |     || |||||||||||||| ||||| | ||| ||| |||||||||| ||  | || || ||||| || ||||| ||||| || ||||| ||||||||||| || ||||
gtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagcatttcaagccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG

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|24205139|gb|BU964392.1|BU964392
EST:     AGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG                         ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACA
genomic: AGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAGgtttgtttat ... acttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACA
EST: gi|15814111|gb|BI786386.1|BI786386
EST:     CAAGCTTTCTGGGGGTGTTGCAGTACTGAAG                         ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACA
genomic: CAAGCTTTCTGGGGGTGTTGCAGTACTGAAGgtttgtttat ... acttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACA
EST: gi|209725420|gb|BW658282.1|BW658282
EST:     AGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAG                         ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACA
genomic: AGTTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAGgtttgtttat ... acttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACA
EST: gi|16344877|gb|BI970472.1|BI970472
EST:     TTACAGGAAAGATTAGCCAAGCTTNNTGGGGGTGTNNNAGTACTGAAG                         ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACA
genomic: TTACAGGAAAGATTAGCCAAGCTTTCTGGGGGTGTTGCAGTACTGAAGgtttgtttat ... acttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatcctatggttttgtcatgataaaactaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG
                                         cctcactttt  CT-rich tract
                      ataaaactaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttatttgagtttaccttgcttgctattaggattttatctggcacttcatcctatggttttgtcatgataaaactaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG