ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gttcgctctgtgcaaattctctaacttgttctcactttgttgatttcctcttcatttcgtaacattttgtgcattgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAA

Basic information

species	Glycine max
transcript	GLYMA17G03550.2
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 3'ss of exon 1

--------------------------------gttcgct--ctgtgcaaattctctaacttgttctcactttgttgatttcctcttcatttcgtaacattttgtgcattgaa-----ttgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAA
                                 |||| |  || |   | || || | |||  | |   |    ||||| |   ||  ||||||    |  |   | |||||       |  |||||||| ||||||||||||||||| || ||||||||||| |||||||| || ||||| || ||||| ||||| ||| | || ||||| |          
gtaaccgacgattcctccatttccatcgcctcattcgatgtctctttgatttatcgatcttcgttttcttcccctgattcctgatttttttcgtttgttcgtcgtctttgaagGATTCGGGGGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGGATCAAGAAGCCCAAGCGCCACCGCCAGA----------

upper sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1

------------------gttcgctctgt----gcaaattctctaacttgttctcac--tttgttgatttcctcttcatttc--gtaacattttgtgcattgaattgc---agAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAA
                  | ||| |||||     | |  | | |   | ||  ||||  |   |  |  ||| | | | |    ||  | ||||||     |   | |   ||||||||| ||||||||||||||||| || ||||||||||| |||||||| || ||||| |||||||| ||||| ||| | || || ||            
gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-----------

upper sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G147791_T01 (Zea mays), 3'ss of exon 1

------------------gttcgctct-gtgcaaattc-tctaacttgttctcactttgttgattt-cctcttcatttcgta------acattttgtgcattgaatt---gcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAA
                  | ||| |||  | | |||   | | | ||       |   ||  |    || || || ||  |        || |||||     |   |   | ||| ||||| ||||||||||||||||| || ||||||||||| | |||||| || ||||| ||||| || || || ||| | || |||||            
gtaattctcaggcaccccgctcgatctcatcctaatcggtgtgattttcgtcttcaccgtcaacccacccctccacttactctgattcgcactttgttggcagGCATCCGGAAGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----------

upper sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G147791_T02 (Zea mays), 3'ss of exon 1

gttcgctctgtgcaaattctctaacttgttctcactttgttgatttcctcttcatttcgtaacattttgtgcattgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAA
||  | | |  |     |||  | | |   | |||    |  | || ||||    |||| |   | |||           | ||| ||||| ||||||||||||||||| || ||||||||||| | |||||| || ||||| ||||| || || || ||| | || |||||            
gtgtgattttcg-----tcttcaccgtcaacccacccc-tccacttactct--gattcgcactttgttggcagGCATCCGGAAGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----------

upper sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G147791_T03 (Zea mays), 3'ss of exon 1

-------gttcgctct-gtgcaaattc-tctaacttgttctcactttgttgatttcctcttc-----atttcg--taacattttgtgcattgaatt---gcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAA
       | ||| |||  | | |||   | | | ||       |   ||  |    | | ||     | |  |  |  || |||||     |   |   | ||| ||||| ||||||||||||||||| || ||||||||||| | |||||| || ||||| ||||| || || || ||| | || |||||            
gcaccccgctcgatctcatcctaatcggtgtgattttcgtcttcaccgtcaacccacccctccacttactctgattcgcactttgttggcagGCATCCGGAAGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----------

upper sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S58_102V6.2 (Physcomitrella patens), 3'ss of exon 1

-------------------gttcgctctgtgcaaattctc--taacttgttctc-actttgttgatttcctcttcatttcgtaacattttgtgcattgaattgcag-
                   |||   | |  |   |||||   ||  | |   |  |  || |  || |   || ||||  ||    |||  | |  |  || ||||   ||||||| ||||| ||||| |||||||| ||||||||||||||||||  ||| |||||||| ||||| |||   ||||  ||     |  | ||      
ttagttcggagatgatttagttgaattttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagt---ttttcattcgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTC------

upper sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S28_307V6.1 (Physcomitrella patens), 3'ss of exon 1

----------------gttcgctctgtgcaaattctctaacttgttctcactttgttga--tttcctcttcatttcgtaacattttgtgcattgaa--ttgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAA
                | |||  ||| || |  | | | |  || |     | |||| |  |||| | ||  | |  | |  |  ||||  ||| |    |     ||||| || || ||||| || ||||||||||||||||||||||||  ||| |||||||| ||||| |||   |||| |||     |  | || |    
tcaggatttgaaacaggctcga-ctgcgccatgtgtttgaagtggtggggttgtgtttacgtttcgttttgttgtacttatgtcctgtgggttggaagcagGTAGAATGGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAG---

upper sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 1

----------------gttcgctctgtgcaaattctc--taacttgttctc-actttgttgatttcctcttcatttcgtaacattttgtgcattgaattgcag-
                |||   | |  |   |||||   ||  | |   |  |  || |  || |   || ||||  ||    |||  | |  |  || ||||   ||||||| ||||| ||||| |||||||| ||||||||||||||||||  ||| |||||||| ||||| |||   ||||  ||     |  | || |    
gttcggagatgatttagttgaattttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagt---ttttcattcgctcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG---

upper sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1

------------------gttcgctctgtgcaaattctctaac-ttgttctcactttgttgatttcctcttcatttcgtaacattttgtgcattgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAA
                  |   ||| ||  |  |    ||    ||||| |  || ||| | | || |  |    |  |     | ||    |  |   |   ||||||| ||||| ||||||||||| || ||||||||||||||||||  ||| |||||||| ||||| |||   |||| ||||    |||  || |    
agcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG---

upper sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1

---------------------gttcgctctgtgcaaattctctaac-ttgttctcactttgttgatttcctcttcatttcgtaacattttgtgcattgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAA
                     |   ||| ||  |  |    ||    ||||| |  || ||| | | || |  |    |  |     | ||    |  |   |   ||||||| ||||| ||||||||||| || ||||||||||||||||||  ||| |||||||| ||||| |||   |||| ||||    |||  ||      
tgcagcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC------

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|12772062|gb|BG236989.1|BG236989

EST:     GCAGAAAACCCTAGCCCAACCGGATCTTCACGACTAGG                         AGATGGC-AAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: GCAGAAAACCCTAGCCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|24205832|gb|BU965085.1|BU965085

EST:     AACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: AACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|58014658|gb|CX701400.1|CX701400

EST:     GCCCAACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: GCCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|208263909|gb|GE065317.1|GE065317

EST:     GCAGAAAACCCTAGCCCAACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: GCAGAAAACCCTAGCCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|254343184|gb|GR859346.1|GR859346

EST:     ATTCTGTTCCGCAGAAAACCCTAGCCCAACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: ATTCTGTTCCGCAGAAAACCCTAGCCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|16280819|gb|BI944162.1|BI944162

EST:     CAGAAAACNCTAGCCCAACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: CAGAAAACCCTAGCCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|17963907|gb|BM270650.1|BM270650

EST:     CCCTAGCCCAACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: CCCTAGCCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|254341697|gb|GR852834.1|GR852834

EST:     CTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: CTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|14990191|gb|BI315864.1|BI315864

EST:     CCCAACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: CCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|209701113|gb|BW652641.1|BW652641

EST:     CCGCAGAAAACCCTAGCCCAACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: CCGCAGAAAACCCTAGCCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|209701112|gb|BW652640.1|BW652640

EST:     AACCCTAGCCCAACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: AACCCTAGCCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|192319416|gb|FK005856.1|FK005856

EST:     GCAGAAAACCCTAGCCCAACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCGC
genomic: GCAGAAAACCCTAGCCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|6667850|gb|AW279301.1|AW279301

EST:     CTAGCCCAACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: CTAGCCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|11274886|gb|BF325211.1|BF325211

EST:     AGAAAACCCTAGCCCAACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: AGAAAACCCTAGCCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|15815077|gb|BI787352.1|BI787352

EST:     CTAGCCCAACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: CTAGCCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|8285210|gb|BE022769.1|BE022769

EST:     AGCCCAACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: AGCCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|192325585|gb|FK019441.1|FK019441

EST:     AATTCTGTTCCGCAGAAAACCCTAGCCCAACCGGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGGCC
genomic: AATTCTGTTCCGCAGAAAACCCTAGCCCAACCGGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

EST: gi|21675358|gb|BQ627709.1|BQ627709

EST:     GGATCTTCACGACTAGG                         AGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC
genomic: GGATCTTCACGACTAGGgttcgctctg ... tgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCC

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tctcactttgttgatttcctcttcatttcgtaacattttgtgcattgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAA

                           tcgtaac  putative branch site (score: 2)
                              taacatttt  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