ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

ggtacaacatccgctctgaaaattgtcagttgttttccactctacagaagtagtttgtgatcattgacttattccttttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG

Basic information

species	Glycine max
transcript	GLYMA18G44460.1
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 6

ggtacaacatcc-gctctgaaaattgtcagttgt-tttccactctacagaagtagtttgtgatcattgacttattccttttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-
|  || |  ||  |||      ||| |||  |||   |   |    || |   | | ||| ||  |  || ||  |  |||   || ||    |     ||||||| ||||||||||| |||||||||||||||||||| || || || ||  | |||||||| ||||| ||||| ||||||||||||||||| 
gtaactatttcaagcttgcttgattttcatctgtgcatgtgcctaccaaatacattctgtaattgt--acctaa-ctgtttaactcattgcactataccagGATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 5

ggtacaacatccgctctgaa-aattgtcagttgttttccactctac-agaagtagtttgtgatcattgacttattccttttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-
|  || |  || |   |||  |||| |||  |||        |||| |     | | ||| |   |  || ||    |||   |  |||    |     |||| || ||||||||||| |||||||| ||||||||||| || || || ||  | |||||||| ||||| ||||| ||||||||||||||||| 
gtaactatttcaggcttgattaattttcatctgtgcaaatgcctaccattttcattctgtaagattgtacctaaatgtttaactcatttgcactataccagGACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5

ggtacaacatccgctctgaaaattgtcagttgttttccactctacagaagtagtttgtg-atcattgacttattccttttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-
        | |   | | | | | ||     | | |   || |     |  | |||||  |||| | ||| | |        | || || | |||   |||| ||||||||||||||||||||||||||||||||||||||||| || ||| | || ||||| ||||||||||| |||||||| |||||||| 
------gtagctattttcatactcgtgtacagatctgagctttg----aacaatttgtacatcagtcactaagt--------tgctgttctatgcc--agGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT

upper sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6

ggtacaacatccgctctgaaaattgtcagttgttttccactctacagaagtagtttgtgatcattgacttattccttttttttcttttttgtgct---ttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-
                 | || || |   |  || |  ||  |   ||  |  | | ||| || | |  ||   |  ||  |   ||  ||| ||     |||||||||||||||||||||||||||||||||||||||| ||||| || ||| | || ||||| ||||| ||||| |||||||| |||||||| 
-----------------gtaactttttcatacttgtgtacatt---gacctgttctttgaacaat-atgtacatcagttgctaagttgctgttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT

upper sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6

ggtacaacatccgctctgaaaattgtcagttgttttccactctacagaagtagtttgtgatcattgacttattcct----tttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-
                |  || || |       ||| | || | ||  | |  |||     | ||  ||||| |      | ||    | ||   | ||  ||||||| ||||||||||||||||| || ||||||||||| || ||||| ||  |||| || |||||||| || || || | |||||||||||| 
---------------gtacaatttctttaaaccttttccctatccaacattttttttcttacttttgcttatactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT

upper sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6

--------------------------------------ggtacaacatccgctctgaa---aattgtcagttgttttccactcta--cagaagtagt--ttgtgatcattgacttattccttttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-
                                        |     || |  | | |    |||   || ||  | |  | | |   | |||| |    ||  |   |  | ||  |       ||     ||   |  |  ||||||||||||| ||||| ||||| ||||| |||||||| || ||||||||| | || || |||||||| || || ||| ||||||||||||| 
gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT

upper sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6

-----------ggtacaacatccgctctgaaaattgtcagttgttttccactctacagaagtagtttgtgatcattgact--tattcctttttt-------------ttcttttttgtgc--tttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-
             |||| |   | ||||      ||| ||    ||||   | | |     |  |   || |  ||  |   | ||| | ||||             || ||| |||||   | |||||||||||||||||||| || |||||||| |||||||| || ||||||||  | || || || ||||| ||||| |||||||| || || || 
gtatttattccattacatctctctctctctgtgatgt-agccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC

upper sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 5

-----------------------------------------------------------------ggtacaacatccgctctgaaaattgtcagttgttt-------tccactctacagaagtagtttgtgatcattgacttattccttttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-
                                                                 |  ||   |  ||    ||  |||   ||| | ||       |||   |||  |     ||||| |||  |  |   |   ||        ||| |  |  |  |||||||||| ||||||||||||||||| || ||||| || || ||||| || ||||| || ||| | || ||  | || |||   || ||||| 
gtaagttttggtgatcgaattatgtttttttaagtgggctccgcatttggcctaattttgaaatggaaactgaacacgtgtagatcatttggagtaggttcatcttatcctagctattgccacggtttg-gatgttcaaaaaaaaactgacaggaatttctctttttgcagGATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGT

upper sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ36040 (Selaginella moellendorffii), 3'ss of exon 5

ggtacaacatccgctctgaaaattgtcagttgttttccactctacagaagtagtttgtgatcattgacttattccttttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-
                               || |        ||  ||  |  ||||| || |   || |  |  ||  |  | |   ||      ||||||||||||| ||||| ||||||||||| ||||| || |||||||| ||  || ||||||| || || ||  | || |||   |||||||| 
-------------------------------gtatgaag----acgaaaacacattgtggtc-tgagctcaaac--ttagtaacgtccgtg-atcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGTGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC

upper sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5

ggtacaacatccgctctgaaaattgtcagttgttttccactctacagaag-tagtttgtgatcattgacttattccttttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-
                                      |      ||||   |  ||||| || |   || |  |  ||  |  | |   ||      ||||||||||||| ||||| ||||||||||| || || || |||||||| ||  || ||||||| || || ||  | || |||   |||||||| 
------------------------------------gtatgaagaagaaaacacattgtggtc-tgagctcaaac--ttagtaacgtccatg-atcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC

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|31467402|gb|CD409430.1|CD409430

EST:     GTATGCTAGAATTATCCCAAAGCTTGGTTTCCCAGCTAAATTTAA                         GGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCAT
genomic: GTATGCTAGAATTATCCAAAAGCTTGGTTTCCCAGCTAAATTTAAggtacaacat ... ttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCAT

EST: gi|9440109|gb|BE440620.1|BE440620

EST:     GTATGCTAGAATTATCCAAAAGCTTGGTTTCCCAGCTAAATTTAA                         GGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCAT
genomic: GTATGCTAGAATTATCCAAAAGCTTGGTTTCCCAGCTAAATTTAAggtacaacat ... ttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCAT

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

acagaagtagtttgtgatcattgacttattccttttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG

                  cattgac  putative branch site (score: 3)
                    ttgacttattcctttt  CT-rich tract
                         ttattccttttttttc  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