ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaagatctaggatgctgttgcacttctttatatcatcatgtcaacgaagctaactttacgtggtcttcag

Basic information

species	Zea mays
transcript	GRMZM2G037185_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G037185_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g08480.1 (Oryza sativa), 5'ss of exon 6

TATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaagatctaggatgctgttgcacttctttatatcatcatgtcaacgaagctaactttacgtggtcttcag
||||||||||||||||||||| || ||||||||||||||||| || |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||   |  | ||| ||   |||||| ||  || |||    ||  || | ||||||||| ||  |  || ||||
TATGCTATTTGAAGTCCACAACGCGGCAGCAGAACGGACTTCACACTGTGGTGTCCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatggacatgtttagaataacgttgcaattacttttat-gcgattccaccaaagctaactctat-tactcatcag

upper sequence: GRMZM2G037185_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G01000.1 (Glycine max), 5'ss of exon 4

TATGCTATTTGAAGTCCACAATGCAGCAGCA-----GAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaagatctaggatgctgttgcacttctttatatcatcatgtcaacgaagctaactttacgtggtcttcag
     | ||| || ||   ||||  ||  ||     || |||  ||| |||||||| |||||||||||||||||||| ||||| |  || || |||||||| ||||||      || |   |   |||   || || |  ||| |    |  ||                           
-----TGTTTAAACTCAGAAATGGTGCTTCAATTCTGAGCGGGTTTCTCATTGTGGGGTTCTGGAGTTCATTGCAGATGAAGGGACTATATATATGCCATACTGGgta-----ggaccagaggaactgaaaca-ttatgaatacctggttaccag--------------------------

upper sequence: GRMZM2G037185_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G00980.1 (Glycine max), 5'ss of exon 5

TATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtc---aagatctaggatgctgttgcacttctttatatcatcatgtcaacgaagctaactttacgtggtcttcag---------------------------------
 ||| | |||||| ||   ||||  ||  | ||  ||  ||| |||||||| |||||||||||||||||||| ||||| |  || || |||||||| |||||| | |   | || ||   |   | | | |   |||  || ||  |           | || |||      |||| |                                  
AATGATGTTTGAACTCAGAAATGGTGCTTCTGAGAGGGTTTCTCATTGTGGGGTTCTGGAGTTCATTGCAGATGAAGGAACTATATATATGCCATACTGGgtaggaccagaggaactgaaacattat-gaataccttgttaccagtagaatggttct-ccaagtttctagtttcttaatgcatgctagtttcttatgagatgttttatacag

upper sequence: GRMZM2G037185_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G05030.1 (Glycine max), 5'ss of exon 6

TATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatg---tcaagatc--taggatgctgttgcacttctttatatcatcatgtcaacgaagctaactttacg----tggtcttcag----------------------------
 ||| | |||||| |||  ||||  || || || |||  ||| |||||||| ||||||||||||||||| || ||||||||||| ||||||||||| |||||| |   |||| |    | |  || |  |  | || |     |  |      ||    | |  ||||  |    | || ||                               
AATGTTGTTTGAACTCCGTAATGATGCTGCCGAGCGGGTTTCTCATTGTGGGGTTCTGGAGTTCATTGCTGAGGAAGGCATGATATACATGCCATACTGGgtaggcattcaaaagtagttgtttgttaatatagttgtacgc-ttgtttcactaatatggttcgctttgagattttagttttttttttttgttgatgctgttttcatatacag

upper sequence: GRMZM2G037185_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G34630.2 (Glycine max), 5'ss of exon 6

TATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatg--tcaagatctaggatgctgttgcacttctttatatcatcatgtcaacgaagctaactttacgt--ggtcttcag-------------------------------
 ||| | |||||| |||  ||||  || || || |||  ||| |||||||| ||||||||||||||||| || ||||||||||| ||||||||||| |||||| |  |  | |  ||   || |  || |  |   | ||   |  | ||| | ||  |   | | | |   || || ||                               
AATGTTGTTTGAACTCCGTAATGATGCTGCCGAGCGGGTTTCTCATTGTGGGGTTCTGGAGTTCATTGCTGAGGAAGGCATGATATACATGCCATACTGGgtaggcattcaaaagtaat-tgtttgtgaatataggtgtaagcttgtttca-ctaatatggttctgctttgagtttttagtttttttaattgatgctgttttcatatacag

upper sequence: GRMZM2G037185_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT2G21270.3 (Arabidopsis thaliana), 5'ss of exon 6

TATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatg--tcaagatctaggatgctgttgcacttctttatatc--atcatgtcaacgaagctaact--ttacgtggtcttcag-----------
 ||||| |||||  | |  ||||| | |   |||||   | | || ||||| || || |||||||||||||||||||||||||| |||||||||||||||||| |  |||   ||     || |  || |      ||      |||||||  ||  | |  |||  ||   || |  |  |           
GATGCTGTTTGAGCTTCGTAATGCTGGAATTGAACGTGTTACACACTGTGGAGTCCTTGAGTTCATTGCAGAAGAAGGCATGATTTACATGCCATATTGGgtaagaatcagtttcctctttgtttgtgaatcgaagtactctggatcatgtggacttaccagactgattgtttgcttctttgatataatccag

upper sequence: GRMZM2G037185_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv03s0038g00750.t01 (Vitis vinifera), 5'ss of exon 6

TATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaagatctaggatgctgttgcacttctttatatcatcatgtcaacgaagctaactttacgtggtcttcag-------------------------------------------------------------
 ||| | || ||| |    ||| | || ||  | |||   || |||||||| |||||||| ||||| || ||||| ||||||||||| ||||||||||||||| |     ||| |  | ||  |||    | |     |  |  ||  |||  |  |  || || ||    || |                                                              
CATGTTGTTCGAACTTAGTAATCCTGCTGCTCAGCGGGTCTCCCATTGTGGAGTTCTGGAATTCATAGCTGAAGAGGGCATGATCTATATGCCATATTGGgtaggc----atccaaaa-gcatttgtctgtataagcctggtattgcaaacatattttgctgtaggtcagttttactactgcagatgtctccagggcactcattcctgttgtgatccttttaattgtttcctgtcag

upper sequence: GRMZM2G037185_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S245_32V6.2 (Physcomitrella patens), 5'ss of exon 5

TATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaagatctaggatgctgttgcacttctttatatcatcatgtcaacgaagctaactttacgtggtcttcag-----------------------------------------------------------------------------------------------------------
 ||| | ||||||||||||||  |  || |    |||||    |||||||| || ||||||||  | ||||| ||||||||||| |||||||| || |||||||   || ||  |  || |  ||| ||||||| | || ||  |    |      ||  | ||| |  |    |                                                                                                            
AATGTTGTTTGAAGTCCACAACCCTTCAACCTTGCGGACAAGTCATTGTGGCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtat---aaaattcatcatcc--ttggacttcttca-attattgttctgaaccgcttatttctac-tactgcaaaaaataatttgagaaaaggatgtgtctcattgacttcgaacttttttgactttaggtgctctgagcagcttgtggtgctgtagatgacgtgtgtgagtggcacatgcag

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|18384255|gb|BM417454.1|BM417454

EST:     GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGG                         ATGATGCAAAATCTTCTGTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT
genomic: GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaag ... tggtcttcagATGATGCAAAATCTTCTTTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT

EST: gi|211152115|gb|FL081689.1|FL081689

EST:     GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGG                         ATGATGCAAAATCTTCTGTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT
genomic: GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaag ... tggtcttcagATGATGCAAAATCTTCTTTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT

EST: gi|71332942|gb|DR803495.1|DR803495

EST:     GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGG                         ATGATGCAAAATCTTCTTTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT
genomic: GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaag ... tggtcttcagATGATGCAAAATCTTCTTTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT

EST: gi|93281779|gb|EB674043.1|EB674043

EST:     GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGG                         ATGATGCAAAATCTTCTTTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT
genomic: GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaag ... tggtcttcagATGATGCAAAATCTTCTTTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT

EST: gi|18384443|gb|BM417642.1|BM417642

EST:     GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGG                         ATGATGCAAAATCTTCTGTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT
genomic: GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaag ... tggtcttcagATGATGCAAAATCTTCTTTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT

EST: gi|87151920|gb|DY396709.1|DY396709

EST:     GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGG                         ATGATGCAAAATCTTCTGTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT
genomic: GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaag ... tggtcttcagATGATGCAAAATCTTCTTTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT

EST: gi|22489686|gb|BU049609.1|BU049609

EST:     GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGG                         ATGATGCAAAATCTTCTGTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT
genomic: GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaag ... tggtcttcagATGATGCAAAATCTTCTTTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT

EST: gi|71766016|gb|DR963953.1|DR963953

EST:     GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGG                         ATGATGCAAAATCTTCTTTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT
genomic: GTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaag ... tggtcttcagATGATGCAAAATCTTCTTTTGCAAGAGGGAGATATGGTGTTCATAAAAAAT

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: 45 (upstream exon), 48 (downstream exon)
Score: 145

TATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaag ... tggtcttcagATGATGCAAAATCTTCTTTTGCAAGAGGGAGATATGGTGTTCATAAAAAATGCCAACCTCCCCAAGGGCACATATGTGAAGTTGCAGCCTCATACAACAG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 150

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 157

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 133

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGCTATTTGAAGTCCACAATGCAGCAGCAGAACGGACTTCGCATTGTGGTGTTCTGGAGTTCATTGCAGAAGAAGGCATGATCTACATGCCATATTGGgtatgtcaagatctaggatgctgttgcacttctttatatcatcatgtcaacgaagctaactttacgtggtcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG