ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtgattgtttagtttattacaaattagctctttgacgcatgtgccaagtagattgaatttgaactctagaacatgttttggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATGCTTTAATG

Basic information

species	Glycine max
transcript	GLYMA06G15520.2
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g64630.1 (Oryza sativa), 3'ss of exon 4

------------gtgattgtttagtttattacaaattagctctttgacgcatgtgccaagtagattgaatttgaactctag-aacatgttttggttttg---cagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATGCTTTAATG------------
            |   |  | |   || ||  ||||| |   ||  |      |||  |  |  |||   |  ||  |||   ||||    |   ||||   ||||||||||| || ||||  ||||| ||||| |||||||||  ||||||||||| |||||||||||||||      | |    | ||               
gtctagtaatatgcactactatttcttctttgaaattggtatttctat-----tgctgatcattttgctctgcaaaactaatgacatccacttaatttgtcacagATGTGGATCTCCAAGGCCGAATACGATGAATCTGGTCCAGGCATCGTCCACATGAAGTGCTTCTAAGTTTGTGGGCAGATTTGTACCATTATCAGCTGAT

upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 4

gtgattgtttagtttattacaaattagct--ctttgacgcatgtgccaagtagattgaatttgaactctagaacatgttttggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAG----AAATGCTTTAATG--------
|| |   ||  |  ||      || || |  |    | ||| ||      |   ||   ||   |   |       |  |   |  | ||||||||||| |||||||| || ||||||||||| |||||| | || || ||| |||||||||||||||            ||  ||||   |         
gtaaaccttacgcctacactttatgaggtagcaagaatgcaggtatttc-tgctttctgttaacatcattcttttggcatctatgctacagATGTGGATCTCAAAGGGAGAGTATGATGAGTCGGGTCCAGCAATTGTTCACCGGAAGTGCTTCTAAGCTCTGGCTTTTTAATCGCTTATCTACAAGGCAG

upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g36650.1 (Oryza sativa), 3'ss of exon 4

gtgattgtttagtttattacaaattagctctttgacgcatgtgccaagtagattgaa------tttgaactctagaacatg--ttttggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATG---CTTTAATG---------
|| || |   | |     |  | |||  |||| ||  ||  | | |  | | | ||        ||||  | |    | |   ||||  || ||||||||||||| |||| || ||| ||||| || ||||| ||| | |||||||||||||||||||||||  |       |  ||   |||| |||         
gtaat-gcaaaatcatccaacagttaattctt-gatacactttctagattgttcgagaaggttcttgacatatgtttctttccttttttttgtgcagATGTGGATCTCAAGGGCTGAGTATGAAGAATCTGGCCCAGCTATCGTCCACAGGAAGTGCTTCTAGATGTGGCCTAGCTGTATCTTTCATGAGAACCCCT

upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 4

-gtgattgtttagtttattacaaattagctctttgacgcatgtgccaagtagattgaatttgaactctaga-acatgttttggtttt---------gcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATGCTTTAATG---------------
  |   | |||  ||     | ||| | ||   | || |||       | |     ||| | |  |  ||| || | |  || | ||         |||||||||||| || ||||| || |||||||| || || || || |||||||||||||| |||||||||  | |   |   |||| | |                 
atttgctatttgattatgccctaataaactagattacacattaattttgaatgcaaaatgttagataaagacacttatcctgttctttttcctgtcgcagATGTGGATATCTAAGGGAGAGTATGATGAATCCGGCCCTTCAATCGTCCACAGGAAATGCTTCTAATCCGA---GCCTTGCTCTGAGTATTTTCGGTGTGCCT

upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 4

---------------------------------------------------------------------gtgattgtttagtttattaca--aattagctctttgacgcatgtgccaa-gtagattgaatttgaactctagaacatgttttggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATGCTTTAATG------------
                                                                         ||||||| ||    |||  || | |   ||| | |  | ||| || | | ||   |||||    || |    || |         ||||||||||| || |||| ||| |||||||| ||||| ||| | || || |||||||||||||||| |||     |      | |    |            
gtaagtccttatcattacagcttcttagatgctcaccagaattagttcataactacttcataaccaatccattttgtttatttgtccacaccaagttgtattttaatggttttgctaatgcacatgtgatttgtttgcttggcattgataaaa----acagATGTGGATATCGAAGGATGAGTATGATGAATCTGGCCCAGCAATTGTTCACAGGAAGTGCTTCTGAGTTTCTCATGCTGCCCTGTGCGTCGGTTTGTACT

upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 4

------------------------------------------gtgattgttt-----agtttattacaaattagctctttgacgcatgtgccaa---gtagattgaatttgaactctagaacatgttttggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAA--GTCA-----AAAAGAAATGCTTTAATG-----
                                           || || |||     | |  |   ||   |||   |  |  | |   |   |   ||  |   | | |||  |  ||  ||| ||||   | ||||||||||||| |||| || ||| ||||| |||||||||||| | || ||||||||||||||||||||   ||||         ||||||| ||  |      
gtaacaccaagtcttccgacggctgttctgtatccacaatctatgtttatttgtgaaaatgcacctcacggtagggttgcggagaaaaggtttatttgtgaagctactctgacattaagtccatcttttccctgtgcagATGTGGATCTCAAGGGCTGAGTATGAGGAGTCTGGTCCAGCTATTGTCCACAGGAAGTGCTTCTAGACGTCACTCCTCGTGGAAATGCCTTTGTTTCATG

upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 4

gtgattgtttagtttattacaa--attagctctttgacgcatgtgccaagtagattgaatttgaactctagaacatgttttggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAA--GTCAAAAAGA---AATGCTTTAATG-------
|| |        |||    |    |||   | | |      || | | | |   |  | ||   ||   ||  | ||||||   | ||||||||||||| |||| || ||| ||||| |||||||||||| | || ||||||||||||||||||||   ||||   ||    ||| ||    ||       
gtaacaccaagttttccggcggctattctgtatctactatctgagtctattttgtgaagttctgacataagttcttgttttccctgtgcagATGTGGATCTCAAGGGCTGAGTATGAGGAGTCTGGTCCAGCTATTGTCCACAGGAAGTGCTTCTAGACGTCACCTAGCCTTAATTCTCCTCTGGAAATAC

upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G104017_T04 (Zea mays), 3'ss of exon 4

------------------------gtgattgtttagtttattacaaattagctctttgacgcatgtgccaagtagattgaatttgaactcta----gaacatgttttggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATGCTTTAATG--------------
                             || |    ||  |     ||| |||  | ||     ||  | | | |     |  ||| |||     ||    |  ||| | |  ||||||||||| || ||||  || |||||||||||||| ||  | ||||||||||||||||||||||| ||     |  | | | | | ||              
gtatgcggttgtttatatctactttcagctgctgcacttcatttgttttaactcagtaacatggttgaaatg-ataacacttccgaattctgttgtgatgtggcattgatgtaccagATGTGGATATCCAAGGAGGAGTATGATGAGTCTGGCCCGGCAATCGTCCACAGGAAGTGCTTCTAGGTTCCGCA--AGTTCCTCATTGTTATCTAGTCTCAA

upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 4

--------------------gtgattgtttagtt--tattacaaat----tagctctttgacgcatgtgccaagtagattgaatttgaactctagaac--atgttttggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATGCTTTAATG--------------
                    || ||| |  ||||  |||  |||||     | |  || |     |     |||    |||  | | ||  |  |  |   | |||   |  | ||||||||||| ||||||| ||| || |||||||| || ||| | || || ||| |||||||||||||||   ||  |     | ||  |               
gttaaaaccttataacacttgttattttccagttgctatggcaaatattccaacctttcggtagttccagtaagctc-ttggttctaaaaacatgctctcgtatttatatgctacagATGTGGATCTCAAAGGCTGAGTACGATGAGTCAGGACCAGCGATTGTTCACCGGAAGTGCTTCTAAGCTCAAGGGC--CCCCTTCGTCCCCATTCTATGTAT

upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G053284_T01 (Zea mays), 3'ss of exon 4

-----------gtgattgttt----agtttattacaaattagctctttga--cgcatgtgccaagtagattgaatttgaactctagaacatgtt-ttg-gttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATGCTTTAATG------------
           || | ||| |    |  | | | |||  |  ||  |||    |||  |     ||| ||  | |||||  | |  | | |||| ||| ||| || |||||||||| || ||||  || |||||||| |||||||||  ||||||||||| |||||| |||| | |     ||   |   |   |             
gttgttagtttgttactgtctcaaaatctaaattcaacgtttctgcttgctttgcagttctagtgtatatgaagtttgatttattaatcttgttattgtgttgtgtagATGTGGATCTCCAAGGAAGAGTATGATGAATCTGGTCCAGGCATCGTCCACATGAAGTGTTTCTGAATTCTGGAGCTGTATATCTGTTATTTACTTATAT

upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 4

------gtgattgtttagtttattacaaattagctctttgacgcatgtgccaagtagattgaatttgaactctagaacatgttttggttttg---cagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATGCTTTAATG------------
       |     ||  |  | ||  ||| |  |   |  |   |||   || |       |   |||| | | |      || ||  | ||   |||||||||||||||||| |||| || |||||||| |||||||| || || |||||||| |||||||||||          |  | |  |             
gtaaaaatcccaattccgcctctttaaaactttcagctccatttatgaaacatgagtgaaaatactgaaattttgttttgtttgtgtgtgtgaatcagATGTGGATTTCAAAGAGTGAGTACGATGAGTCAGGTCCATCGATTGTTCACAGGAAATGCTTCTAAGTGTGTCTTGTCTTATCTGGTTCGTGGTGGTGAG

upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 5

gtgattgtttagtttattacaaattagctctttgacgcatgtgccaagtagattgaatttgaactctagaacatgttttggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATGCTTTAATG--------------
||||||  ||  ||| ||     || | | ||  ||  |||     | |   ||        |  |||  |    ||||| |  | ||||||||||| |||||||||||||||||||| |||||||||||||| |||||||||||||||||||||||  || | || |||||| |||              
gtgatt--ttcattttttgttt-ttggttttt--acaaatggtttgattcttttattgcatgatactaacatgctttttgttggtacagATGTGGATCTCAAAGGGTGAATATGATGAATCTGGTCCATCCATTGTCCACAGGAAGTGCTTCTAAGT--AATACAAGTGCTTTGATGGTGAGTTCCTTTTT

upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 3

gtgattgtttagtttattacaaattagctctttgacgcatgtgccaagtagattgaatttgaactctagaacatgttttggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATGCTTTAATG
              ||  ||||      |||||  | | | |  |   |        |||    |||      | || |  ||| ||||||||||||| |||||   || || |||||||| |||||||| || || ||||| |||||||||||                       
-------------gtaccacaac---attcttttgctcgtttttcttatcagccttgttt---ttct------ttttcttttttcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------

upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3

gtgattgtttagtttattacaaattagctctttgacgcatgtgccaagtagattgaatttgaactctagaacatgttttggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATGCTTTAATG
              ||  ||||      |||||  | | | |  |   |        |||    |||      | ||    | | ||||||||||||| |||||   || || |||||||| |||||||| || || ||||| |||||||||||                       
-------------gtaccacaac---attcttttgctcgtttttcttatcagccttgttt---ttct------ttttcgtttctcgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------

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|17020743|gb|BM091777.1|BM091777

EST:     GTGTTTGGATTGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAGCAG                         ATGTGGATATCGAAGGGTGAATATGATGAGTCTGGTCCATCCATTGTCCAC
genomic: GTGTCTGGATTGGAGGATCAATCCTTGCGTCCCTCAGCACCTTCCAGCAGgtgattgttt ... ggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCAC

EST: gi|193719405|gb|FK651835.1|FK651835

EST:     GTGTCTGGATTGGAGGATCAATCCTTGCGTCCCTCAGCACCTTCCAGCAG                         ATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCAC
genomic: GTGTCTGGATTGGAGGATCAATCCTTGCGTCCCTCAGCACCTTCCAGCAGgtgattgttt ... ggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCAC

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

acgcatgtgccaagtagattgaatttgaactctagaacatgttttggttttgcagATGTGGATTTCAAAGGGTGAATATGATGAGTCTGGTCCATCCATCGTCCACAGGAAGTGCTTCTAAGTCAAAAAGAAATGCTTTAATG

 ctttgac  putative branch site (score: 4)
                 attgaattt  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