ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtgggtgttctcattgcaatccacgtttctgtttaatctaggatcttgtttgtttattttatgaaaaattccatgtttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGAGCTACATGTAAATTCCATCACCCAGAACTTGGTTTCCTTACGGAGACGC

Basic information

species	Zea mays
transcript	GRMZM2G069009_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G069009_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g15350.1 (Oryza sativa), 3'ss of exon 4

gtgggtgttctcattgcaatccacgtttctgtttaatctaggatcttgtttgtttattttatga-aaaattccatgtttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGAGCTACATGTAAATTCCATCACCCAGAACTTGGTTTCCTTACGGAGACGC
||| |     ||||| | ||| |  ||  | || ||     |  ||   || || ||||| |||  ||||| | | |    |||||||||| || || ||| |||| ||  | |||||||| |||||||| |||||| |||||||||||||||||||||||||| |||||    || | ||||| |
gtgagataattcatt-cgatcaa--ttcttattaaagtagtggcctgcctttttcattttctgatgaaatttcttat---gtgcagGGTGAGAAAGATTGTACCTACTATGTCAAAACTGGCCATTGCAAATTTGGATCTACATGTAAATTCCATCACCCAGAAATTGGTGGAGTTTCAGAGACAC

upper sequence: GRMZM2G069009_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G28820.1 (Glycine max), 3'ss of exon 4

---------------------------------gtgggtgttctcattg-caatccacgtttctgtttaatctaggatcttgtttgtttattttatgaaaaattccatgtttaatg-cagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGAGCTACATGTAAATTCCATCACCCAGAACTTGGTTTCCTTACGGAGACGC
                                  | ||  | ||  |      ||    ||  | | | |||  |||  |  |||| |     | ||||   ||  |  | | ||  |||||||| ||||| |||||||||||  ||||||| ||||| ||||||||||| || || |||||||||||||| ||||  | || |  | |        | |
gtctgtatcactttttgtatttactacataaggctaggcatgcttttgaatgttctgttttgttttctgatcatggaaatattttgatccgagtttgaatgtttataaatatgataacagGGTGAGAAGGAGTGTTCCTATTATGTGAAAACAGGACAATGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCAGTTCCTGCTGGCATCCAAATTCCAC

upper sequence: GRMZM2G069009_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G37980.1 (Glycine max), 3'ss of exon 4

-------------------------------gtgggtgttctcattgcaatcca-cgtttctgtttaatctaggatcttgtttgtttattttatga--aaaattccatgtttaatg-cagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGAGCTACATGTAAATTCCATCACCCAGAACTTGGTTTCCTTACGGAGACGC
                                |  |||| ||   || | |     ||  || |||     | |||  ||   ||||  || |      || || | ||  | ||  |||||| | || || |||||||||||| ||||||||||||| ||||||||||| || || |||||||||||||| ||| | | ||    | |    |      
gtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactcttttcctaacgatgatggaagttttgttcaaacttgaattttcgtgcatgataacagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG

upper sequence: GRMZM2G069009_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G02720.2 (Glycine max), 3'ss of exon 3

---------------------------------gtgggtgttctcattgcaatccacgtttctgtttaatctaggatcttgtttgtttatttt--atgaaaaattccatgtttaatg-cagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGAGCTACATGTAAATTCCATCACCCAGAACTTGGTTTCCTTACGGAGACGC
                                  || ||| | |        |    ||  || |||     |||||  ||   ||||  ||   |    || || | ||  | ||  |||| ||| || || |||||||||||  ||||||||||||| ||||||||||| || || ||||||||||| || ||| | | ||    | |    |      
gtctgtatcagtttgtgtttattgcgtaaaattatgcgtgctttgggaatg-ttggtgtcactcttttcctaaggatgatggaagttttgttctaacttgaattttcgtgcatgataacagGCTGAGAAAGAGTGTTCCTATTATGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCACCATCCACAGCCTGCAGGCGTCCAAGCTCTAG

upper sequence: GRMZM2G069009_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G10230.1 (Glycine max), 3'ss of exon 4

-------------------------------------gtgggtgttctcattgcaatccacgtttctgtttaatctaggatcttgtttgtttattttatgaaaaattccatgtt-taatg----cagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGAGCTACATGTAAATTCCATCACCCAGAACTTGGTTTCCTTACGGAGACGC
                                       | ||||| |        ||    ||  | | | |    |||     |||| |     | ||||   ||  |  |  |||||    |||||||| ||||| |||||||||||  ||||||| ||||| ||||||||||| || || |||||||||||||| ||||  | || |  | |        |  
gtctgtgtcacttttttgaatttacttacataaggctaagagtgttttgtgaatgttcagttttgttttctgacagtggaaagattttgatctgaatttgaatgtttataaatgataatgataacagGGTGAGAAGGAGTGTTCCTATTATGTGAAAACAGGACAATGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCAGTTCCTGCTGGCGTCCAAATTCCAG

upper sequence: GRMZM2G069009_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0020g01650.t01 (Vitis vinifera), 3'ss of exon 4

----gtgggtgtt----ctcattgcaatccac---gtttctgtttaatcta---ggatctt----------gtttg---tttattttatgaaaaattccatgt-ttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGAGCTACATGTAAATTCCATCACCCAGAACTTGGTTTCCTTACGGAGACGC
    |||  ||||    ||  ||  |||| |    |||  ||||  || ||   | |||            |||||   || | ||     |||  |  || | ||  | ||||||||||| || || ||||| ||  |||| || |||| |||||||||||| |  ||||||||||||||||| ||| | |  | |  | |      | |  
gtctgtgtttgttgcaactttttttaatctatcctgttaatgttagatttattggaatcacatagcctgaagtttgcagttaagttggctcaaagcttgatatgttgctacagGGTGAAAAAGAGTGCTCCTACTATGTGAAGACAGGACTTTGCAAGTTTGGTGAAACATGTAAATTCCATCATCCACAGCCAGATAGCATACAACTGTCAA

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|78082473|gb|DV510885.1|DV510885

EST:     GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTG                         GGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA
genomic: GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTGgtgggtgttc ... tttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA

EST: gi|94476471|gb|EB705429.1|EB705429

EST:     GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTG                         GGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA
genomic: GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTGgtgggtgttc ... tttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA

EST: gi|149005039|gb|EE039564.2|EE039564

EST:     GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTG                         GGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA
genomic: GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTGgtgggtgttc ... tttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA

EST: gi|91049855|gb|EB160273.1|EB160273

EST:     GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTG                         GGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA
genomic: GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTGgtgggtgttc ... tttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA

EST: gi|148956932|gb|EC902865.2|EC902865

EST:     GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTG                         GGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA
genomic: GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTGgtgggtgttc ... tttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA

EST: gi|149094715|gb|EE180267.2|EE180267

EST:     GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTG                         GGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA
genomic: GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTGgtgggtgttc ... tttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA

EST: gi|71418361|gb|DR804412.1|DR804412

EST:     GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTG                         GGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA
genomic: GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTGgtgggtgttc ... tttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA

EST: gi|76937022|gb|DV175010.1|DV175010

EST:     GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTG                         GGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA
genomic: GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTGgtgggtgttc ... tttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA

EST: gi|74232341|gb|DT640255.1|DT640255

EST:     GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTG                         GGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA
genomic: GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTGgtgggtgttc ... tttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA

EST: gi|149087101|gb|EE176640.2|EE176640

EST:     GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTG                         GGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA
genomic: GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTGgtgggtgttc ... tttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA

EST: gi|76286604|gb|DV026172.1|DV026172

EST:     GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTG                         GGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAAGTTTG
genomic: GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTGgtgggtgttc ... tttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAA-GTTTG

EST: gi|78114960|gb|DV533348.1|DV533348

EST:     GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTG                         GGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA
genomic: GTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTGgtgggtgttc ... tttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGA

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

TGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGATCATCCCAGGGAGGGTGGTTTTGTACCTGTCACATTGAACAGCGGTGGATTCCCCCTGCGTCTGgtgggtgttc ... tttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGAGCTACATGTAAATTCCATCACCCAGAACTTGGTTTCCTTACGGAGACGC

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 38

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtttaatctaggatcttgtttgtttattttatgaaaaattccatgtttaatgcagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGAGCTACATGTAAATTCCATCACCCAGAACTTGGTTTCCTTACGGAGACGC