ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaatttctgtaaataaatccatagtgaacattatgtctataccgccatgttcgagaaaaaaatgtctatacatgaacagttgggggcatttctt...

Basic information

species	Zea mays
transcript	GRMZM2G064366_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G064366_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g34360.1 (Oryza sativa), 5'ss of exon 3

GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaatttctgtaaataaatccatagtgaacattatgtctataccgccatgttcgagaaaaaaatgtctatacatgaacagttgggggcatttctt--
|| |||||||| || || ||  |||||||||||||||| || || ||||||||||| || ||||| ||||||||||||||||||||||||||||||||||||||||||   |   | |||| |||||| | |||   ||  |  | | ||||||  | |     |    |   |||    |  |      | ||||  
GCTAGGAGGAGCTCAGTAAAGCTGGATATATACAGAAAATTTACTAATGCATTGGCGGTATCTGTAATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaatttgactttgttaatcaatagtgcatattggctcactgac-ctatgttcctggattggttaatcagtaatgtggtgc-gtattagtctcttaa

upper sequence: GRMZM2G064366_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G19670.1 (Glycine max), 5'ss of exon 3

GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaatttctgtaaataaatccatagtgaacattatgtc-tataccgccatgttcgagaaaaaaatgtctatacatgaacagttgggggcatttctt--
||||   | |||||||| || ||||||||||| || |||||| |||||||||| || ||  | |||||  | |||||||| ||||| || ||||||||| |   ||   |||   | |||  |      || |  |||  |  |   |     | ||      |    | | | |  ||| | |      |||||    
GCAAAACGAAGTTCTGTTAAGTTGGATATATATAGGAAGTTCTCAAATGCATTAGCAGTAACGGTGATCTCCTCAGTTGCTTGGATAGGATATGAGgtaaggctataattgtgtttgaat--aacacctacttcttgtaatgaataactgaaattgatgttttatccacca-aaaaaaactgatatccatatttcactg

upper sequence: GRMZM2G064366_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G05370.1 (Glycine max), 5'ss of exon 3

GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaatttctgtaaataaatccatagtgaacattatgtc---tataccgccatgttcgagaaaaaaatgtctatacatgaacagttgggggcatttctt
||||   | |||||||| || ||||||||||| || |||||| |||||||||| || ||  |||||||  | |||||||| |||||||| ||||||||| |    | | | ||  | | |  ||  || |||  | ||    | |||  |       ||  ||   |  |  ||   | | |          |  |   
GCAAAACGAAGTTCTGTCAAGTTGGATATATATAGGAAGTTCTCAAATGCATTAGCAGTAACTGTGATCTCCTCAGTTGCTTGGATTGGATATGAGgtaag-gcttatatttagtttattttatcttgcacaaaaagtagcatgtacttcttgtaatgaataactgaaattgatgttttatccaccaaaaaaaactg--

upper sequence: GRMZM2G064366_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv12s0034g01090.t01 (Vitis vinifera), 5'ss of exon 3

GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaatttctgtaaataaatccatagtgaacattatgtctataccgccatgttcgagaaaaaaatgt-------ctatacatgaacagttgggggcatttctt
|||| |||||||||||| ||  ||||||  ||||| |||||| ||||| | || || ||| | ||||| ||||||||||  ||||| || |||||||||||     | | || || | |    | ||    |||  | | ||| |    | ||   | |    ||||        ||||  | | ||  ||     | |    
GCAAAGAGGAGTTCTGTTAAGCTGGATACCTACAGGAAGTTCTCAAATTCTTTAGCAGTTGCAGTGATTGCTTCAGTTGTTTGGATAGGATATGAGgtatgt--tctccagtgaagacacttgtggttttgatt--ggcaataacattgttttactgtagtttatgtgcttaatttatattttaccatgtgaaaaaaatg---

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|67024546|gb|CO453295.1|CO453295

EST:     ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|21891783|gb|BQ744996.1|BQ744996

EST:     ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTTCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|148967311|gb|EE018517.2|EE018517

EST:     ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|76289905|gb|DV029473.1|DV029473

EST:     ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|71314489|gb|DR793872.1|DR793872

EST:     TTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: TTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|22491183|gb|BU051106.1|BU051106

EST:     ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|83278764|gb|DV942772.1|DV942772

EST:     ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|148990960|gb|EE032390.2|EE032390

EST:     GATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: GATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|211398906|gb|FL435802.1|FL435802

EST:     CTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: CTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|149112569|gb|EE295431.2|EE295431

EST:     ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|211376336|gb|FL031209.1|FL031209

EST:     ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|19272383|gb|BM888639.1|BM888639

EST:     ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|19272497|gb|BM888753.1|BM888753

EST:     ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|148959137|gb|EE010606.2|EE010606

EST:     ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|211464044|gb|FL176493.1|FL176493

EST:     ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|148960354|gb|EE153613.2|EE153613

EST:     ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

EST: gi|148971674|gb|EE022398.2|EE022398

EST:     ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG                         GTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG
genomic: ATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGG

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: 136

GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaat ... cattttgcagGTCTATTTCAAAGCGACAGACCCCTTCAGTGAGAGGTGGCAGAGCGCATGGATCATAACTGCCTTCTGGGATGTCCTTGCGTTTGTGTTGCTTCTTGTGA

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 133

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 174

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 256

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAGgtatgcaaatttctgtaaataaatccatagtgaacattatgtctataccgccatgttcgagaaaaaaatgtctatacatgaacagttgggggcatttctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaat