ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtttgtggtgcag

Basic information

species	Zea mays
transcript	GRMZM2G368908_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 2

TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtttgtggtgcag
|||||||||| ||||||||||||||||| |||||||||||||| || || |||||||| ||||||||||| ||||||||||||||||| |||||||||| || |  || |  ||  |   |||| | ||||| |||||  |  |||| |||||| |||| ||||      ||||  | ||| ||
TGCCGTTTGAAGAGGATGACAAGGATCCGAGGATCTGGTTCCTCGATCATAATTACCACGAATCGATGTTTTCCATGTTCAAGAGGATCAACGgtatgcagtttgcaagtcttccat--ttgtttgacctgccctgtgtaactgattgtgttgtactgacgagc------tgttcttcgtgtag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA20G03160.1 (Glycine max), 5'ss of exon 1

TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtt---tgtggtgcag-------
                      ||||||||  || ||||| |||||||| |||||||||||||||||||| |||||||| || || || || ||||||  |||   || || |       | |||    |  | |    |      ||| || ||    ||| |||| | | ||   | ||||  |        
----------------------GGATCCTAACATTTGGTTTCTTGACCATAATTACCATGAATCGATGTTTTCCATGTTTAAAAGAATAAATGGTATGA-GTAG-GAATTTTTTTCCTTTTCTTgtatgtctttttcaattgaagatctcttatctaattgaacatgggtttttctttttggtttacaacaaag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA18G03360.1 (Glycine max), 5'ss of exon 2

-TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtt--tgtggtgcag-
 |||| ||||| || ||||||||||||||||| |||||||| ||||||||||||||||||||||||||||| |||||||| || || || || ||||||  |||   ||||| |       | |||    |    | |  |      ||| |  ||    ||| |||| | | ||  | ||||  |  
GTGCCCTTTGAAGAAGATGACAAGGATCCTAGCATCTGGTTTCTTGACCACAATTACCATGAATCGATGTTTTCCATGTTTAAAAGAATAAATggtatga-gtag-gaaattttttccttttcttgtatgtctcttttaattgaatatctctgatctaattgaacatgggtttttcttttggtttaca

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 2

TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtttgtggtgcag--
|||| ||||| || ||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||| |||||||| || || || || |||| |       ||| || ||  |  ||  |  | ||| |      |    || |  |  ||    ||| |||    | ||| ||||  |   
TGCCCTTTGAAGAAGATGACAAGGATCCTAGCATCTGGTTTCTTGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtaggaaaatttttccttttcttgtatgtctgtttca-attgaatatgcc-tgatctaattgaacattttttttttttggtttacag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 2

TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtttgtggtgcag
|||| ||||||||||||||||| ||  | || || ||||| ||||| ||||| ||||| || ||||||||   |||||||||||| ||||| |||||  ||  ||   |       ||| |   | |  |  | ||||  | |  |  | ||   |||||   ||| |  || ||   |     
TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgtat--tgc-tcgggaaatataatgcttaa-gagtata-tatgtggaaagcctcttttttgactgattttcat-atttgctttcag-----

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 2

TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtttgtggtgcag
|||| ||||||||||||||||| || || || |||||||| ||||| ||||| |||||||| || ||||||  |||||||||||| ||||| |||||  | |    ||| |   | ||| | |   |  |      |  || | | ||  |  |  |    | ||  | ||  |||   | |||
TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctcaggaaact---gatgcttatactgtttatgacattgta-gaaatccatgctttt----aacactacctacttgcttttcag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 5'ss of exon 2

TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtttgtggtgcag
|||| ||||| || ||||||||||| || || || || || ||||||||||| ||||| ||||| ||||| |||||||||||||| || || |||||  |   |   || |   |  |  | ||     | |  | |  ||||||   |||| |    ||| | ||   |  |   || | |||
TGCCCTTTGAAGAAGATGACAAGGACCCAAGTATATGTTTTCTTGACCACAACTACCACGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattattggttgtaagtgatgaggtatctt----ttacaat-ttttatggacaatgtttt----atgggaatttacaataattgtttcag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 2

TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtttgtggtgcag
|||| ||||| || ||||||||||| || || || ||||| ||||||||||| || |||||||| ||||| |||||||||||||| || || |||||  | | ||  || |   |  | ||     || | |  | |  |||||    | |  |   |      ||||  |||||  |      
TGCCCTTTGAAGAAGATGACAAGGACCCAAGCATATGGTTTCTTGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttttcgtaaatgatgaggtctc----gcttacaat-ttttatgggcgatttcttatgggaatttatgatttgtttcag------

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 2

TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtttgtggtgcag----------------------------------------------------------------------------------------------------------------
|||| |||||||| |||||||||||| | || || |||||| | |||||||| || |||||  | ||||||  |||||||||||| ||||||||||| || ||  |   ||||     ||   ||       ||| ||   | | ||   |                ||   || | ||||                                                                                                                   
TGCCCTTTGAGGAAGATGACAAGGATGCCAGCATATGGTTCTTGGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattct-tactac--ttctttcctccaactgattaacttctttgtagttgtttggatgaagaacgcagctgcaagt--ttagcggtgtgttttaaccaatattttctaattttgactggtatgtctcgtaacattttgagtatggcagatttgttaaatctgtttgtggtaaaactgactgttgtaagacgtgtttgctcag

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|149042715|gb|EE047230.2|EE047230

EST:     TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG                         CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA
genomic: TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgta ... tgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA

EST: gi|88755238|gb|DY539379.1|DY539379

EST:     TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG                         CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA
genomic: TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgta ... tgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA

EST: gi|211358110|gb|FL397036.1|FL397036

EST:     TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG                         CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAASACTAAGGGAG
genomic: TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgta ... tgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAA-ACTAAGGGAG

EST: gi|71301807|gb|DR786975.1|DR786975

EST:     TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG                         CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA
genomic: TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgta ... tgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA

EST: gi|211163165|gb|FL410935.1|FL410935

EST:     TGACCACAATTATCATGAGTCCATGTTCTCCATGTTCAAGAGGATTAACG                         CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAGCTAAGGGAGA
genomic: TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgta ... tgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA

EST: gi|15208970|gb|BI430854.1|BI430854

EST:     TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG                         CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA
genomic: TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgta ... tgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA

EST: gi|20507024|gb|BQ279450.1|BQ279450

EST:     TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG                         CCAAGGAGCATGTTGCTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA
genomic: TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgta ... tgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA

EST: gi|148973687|gb|EE024808.2|EE024808

EST:     TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG                         CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA
genomic: TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgta ... tgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA

EST: gi|18964870|gb|BM661257.1|BM661257

EST:     TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG                         CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA
genomic: TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgta ... tgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA

EST: gi|22490364|gb|BU050287.1|BU050287

EST:     TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG                         CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA
genomic: TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgta ... tgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA

EST: gi|26456618|gb|CA828201.1|CA828201

EST:     TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG                         CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA
genomic: TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgta ... tgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGA

EST: gi|211186910|gb|FL380819.1|FL380819

EST:     TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG                         CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAG
genomic: TGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgta ... tgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAG

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: 89

TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgta ... tgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 139

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 123

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtttgtggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT