ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CGTCTCCTCGTCCGTCGGTCCCGAGTACTACGTCGGGATACTTTCCTTCGTTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctgaattgatctcatggattaagatacggaattgaaagtgttgcacttgtttcaattagtgattcagggtggtattcaggagatcagttcggga...

Basic information

species	Zea mays
transcript	GRMZM2G104373_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 5'ss of exon 1

CGTCTCCTCGTCCGTCGGTCCCGAGTACTACGTCGGGATACTTTCCTTCGTTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtat--atctgaat----------tgatctcatggattaagata-cggaattgaaagtgttgcacttgtttcaattagtgattcagggt--ggtattcaggagatcagttcggga
|||||| ||||||||||| || || ||||| || || ||| | || ||||| || ||||||||||||||||| || ||||||||||||||||| ||||||||||  || || ||          |   || |||||||     |  || |||| |||     ||||       || |||  |||| |||  |||  |  ||              
CGTCTCGTCGTCCGTCGGGCCGGAATACTATGTTGGCATATTATCATTCGTCGACAAGGACCAGCTCGAGCCAGGGTGTGCCATTCTGATGCATAACAAGgtattaatgtgtataatttccccttttcctgatggattggttcagtgggattggaagcaccacactaacac--atcagtagttcatggtttggtgattgggt-------------

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 1

CGTCTCCTCGTCCGTCGGTCCCGAGTACTACGTCGGGATACTTTCCTTCGTTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctgaattgatctcatggattaagatacggaattg--aaagtgttgcacttgtttcaattagtgattcagggtggtattcaggagatcagttcggga
 |||||||| ||||| || || |||||||| ||||| || || || |||||||||||||| ||| | |||||||| ||||| ||| ||||||| || ||||| |  || | | | | |  |   |||      |  |||    || ||       |      |||||  || |    |  |    |||   | | || | | 
TGTCTCCTCCTCCGTTGGGCCTGAGTACTATGTCGGAATCCTGTCTTTCGTTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttacttactcgctttactcttttattggtggtgattattgaaatgaaaagtatccagttattagaaatacctaat--tgcctagggtttgactttgagg

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA19G35510.1 (Glycine max), 5'ss of exon 1

CGTCTCCTCGTCCGTCGGTCCCGAGTACTACGTCGGGATACTTTCCTTCGTTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctgaattgatctcatggattaagatacggaattgaaagtgttgcacttgtttcaattagtgattcag-ggtggtattcaggagatcagttcggga--
 || || || || || || ||||||||||| || || ||  | || ||||| |||||||| ||||||||||||||||| || ||| ||||||| |||||||||    |    |   ||  ||  ||     |  |  ||   || |||    ||| || | |     |||  | | |||  ||  || |    |   |||   
AGTTTCGTCCTCGGTGGGGCCCGAGTACTATGTTGGTATCTTGTCTTTCGTCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAGgtagggttagggtatgctgctgatttgttgaattgtttt---agcgttttgattgattgactgccctattttgtgatggattttggggggggggggggggggg

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 1

CGTCTCCTCGTCCGTCGGTCCCGAGTACTACGTCGGGATACTTTCCTTCGTTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctgaattgatctcatggattaagatacggaattgaaagtgttgcactt-gtttcaat-tagtga-ttcagggtggtattcaggagatcagttcggga--
||| || || || || || ||||||||||| || || ||  | || |||||||||||||| |||||||| |||||||| || ||| ||||||| |||||||||    |    |  | |  ||   | |      ||||||    | ||||  || | || |||  | | | ||   | |||  ||  ||  |    || | ||  
CGTTTCGTCCTCGGTGGGGCCCGAGTACTATGTTGGTATTTTGTCTTTCGTTGATAAGGATCAGCTCGAACCTGGATGCGCTATTTTGATGCATAACAAGgtagggttagggttttgttttg--ctgattggttgaattg---tttttgcgttttgattgaatgcactaagtttgtgatggattttgggttagggtttagtgatt

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 1

CGTCTCCTCGTCCGTCGGTCCCGAGTACTACGTCGGGATACTTTCCTTCGTTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctgaattgatctcatggattaagatacggaattgaaagtgttgcacttgttt-caattagtgattcagggtggtattcaggagatcagttcggga
 || || || || || || || ||||||||||| |||||  | |||||||||||||| || ||||| || ||||||||| | ||| ||||||| || ||||||| |   | | |   | | | ||   | |   |   |||     || |  |||| |    ||   |||| ||||| |       |   |  ||| |   
TGTTTCTTCTTCTGTTGGACCTGAGTACTACGTTGGGATTTTGTCCTTCGTTGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTGATGCATAATAAGgtatgtgaaattagggtttaagaatcttgtttttgttgtga-----ttacgattgtgtgttgttgtggatttagggttgctgatttgttttatgttag---

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 1

CGTCTCCTCGTCCGTCGGTCCCGAGTACTACGTCGGGATACTTTCCTTCGTTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctgaattgatctcatggattaagata--cggaattgaaagtgttgcacttgtttcaattagtgattcagggtggtattcaggagatcagttcggga-
||| || |||||||| ||||| ||||| || || |||||  | || || ||||||||||| |||||||||||||| || |||||||| |||||||| |||||||       ||    |   || ||| || |    || |||||| | |||   |||      |||||  || |  |||| | |           || |||  
CGTGTCGTCGTCCGTGGGTCCGGAGTATTATGTGGGGATTTTGTCGTTTGTTGATAAGGATCAGCTCGAGCCTGGTTGCGCCATTCTTATGCACAATAAGgtatggggattttagggtttggggttaggagagtttgatttgaaattcttg-gtttgaaaaggttagt--tttattgtggaaatgttttttgggatttggggt

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|76917638|gb|DV166931.1|DV166931

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|20802781|gb|BQ293831.1|BQ293831

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|71318158|gb|DR795841.1|DR795841

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|148930980|gb|EC873506.2|EC873506

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|148934976|gb|EC879019.2|EC879019

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|32803543|gb|CD955779.1|CD955779

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|26559053|gb|CA831288.1|CA831288

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|26558330|gb|CA830565.1|CA830565

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|148990307|gb|EE031907.2|EE031907

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|87155767|gb|DY400556.1|DY400556

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|21987644|gb|BQ779172.1|BQ779172

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|148980753|gb|EE027320.2|EE027320

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|61117979|gb|DN558940.1|DN558940

EST:     GGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: GGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|149082557|gb|EE171753.2|EE171753

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|149110575|gb|EE190490.2|EE190490

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|22542130|gb|BU092568.1|BU092568

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|61117978|gb|DN558939.1|DN558939

EST:     CCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: CCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

EST: gi|32831887|gb|CD971565.1|CD971565

EST:     TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAG                         GTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT
genomic: TTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCT

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 142

CGTCTCCTCGTCCGTCGGTCCCGAGTACTACGTCGGGATACTTTCCTTCGTTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctga ... tttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCTGTGATGAAAGTTGAAAAGGCACCTTTGGAGTCTTATGCTGACATTGGTG

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 249

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 206

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTCTCCTCGTCCGTCGGTCCCGAGTACTACGTCGGGATACTTTCCTTCGTTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctgaattgatctcatggattaagatacggaattgaaagtgttgcacttgtttcaattagtgattcagggtggtattcaggagatcagttcggga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC