ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgtaataatttttattgttgtgacttgtgacacctgtttcaagatgtccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA

Basic information

species	Zea mays
transcript	GRMZM2G111355_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 23

gtatgtaa-taatttttattgttgtgacttgtgacacctgttt---caagatgtccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA
||||| || |  |||||||| ||   || | | |    | |||   |   || |  | ||| ||    |||   |||||||           ||  |||| || || ||||||||||||||| ||||||||||||||||| |||||||||||||| ||||| || |||||||||||||||||||||||||||||||||||||| || || 
gtatgcaaattgtttttattcttcataccttttaattttatttcttctgaatctttaaatccatctattgattgcttacatag-------aaatcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT

upper sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 23

gtatgtaa-taatttttattgttgtgacttgtgacacc--tgtttcaagatgtccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA
||||| || |  |||||||| ||   |||| | |      |  |||   || |  | ||| || |  |||   |||||||           ||  |||| || || ||||||||||||||| ||||||||||||||||| |||||||||||||| ||||| || |||||||||||||||||||||||||||||||||||||| || || 
gtatgcaaattgtttttattcttcatacttttaattttatttcttctgaatctttaaatccatcgattgattgcttacatag-------aaatcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT

upper sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 22

gtatgtaataatttttattgttgtgacttgtgacacctgtttcaagatgtccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA
                 |||| |||  |  | | |  | |||     | || | ||  ||| ||    || | | ||| | | || ||   ||||    || |||| ||||| |||||||| |||||||||||||| ||||| ||||||||| | || || |||   || ||||||||||| ||||| || || || || || || 
---------------gtttgtggtgtatatttatatttttttt----tctctaaat-gattatccttggattca-atgcttacat-gctcatatt-gggattacagATATGTTGTTGAGAGGATGGATGGTGATCTTTGGGAGAAAGTTCTTAACCCTGATAATACCTACAGAAGGCAACTTATTGATCAGGTTGTATCTACAGCT

upper sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 23

gtatgtaataatttttattgttgtgacttgtgacacctgtttcaagatgt-ccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA
    |||       | | | | | |       |    || | |   ||   ||| ||||||| |||    | ||  |  |||| ||  | | |||||  | |||||| ||||| ||||||||||||||||||||| | |||| |||||||||| | || || |||||||||||||||||||| ||||| || || || || ||||| 
---agtacactccgtcactttagaggagctctatttgtggtccttaatccaccaaatcaattttct--ttaattcaacattcacat-acttatattttga-tgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT

upper sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 23

----gtatgtaataatttttattgttgtgacttgtgacacctgtttcaagatgtccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA
       |     | |||  |        | ||||||  | |  | ||      ||| ||||||| |||    | |   ||||||| || || | ||||    ||||||| ||||| ||||||||||||||||||||| | |||| |||||||||| | || || |||||||||||||||||||| ||||| || || || || ||||| 
ctgcacctccgtcactttagaggagctatatttgtgatccttaataca------ccaaatcaattttct--ttaatacaatgttcacat-gcttatatt-gtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT

upper sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 22

gtatgtaataatttttattgttgtgacttgtgacacctgtttcaagatgtccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA
                 |||| |||  |  | | |  | ||||   | ||    |||  | |  | |   |||||||| | ||||||            || |||| ||||| |||||||| |||||||||||||| ||||| ||||||||| | || || ||||  || ||||||||||| ||||| || || || || || || 
---------------gtttgtggtgtatatttatatttttttctctaagtaattatccttggattcaatgcttacatgcttatattg----------ggattacagATATGTTGTTGAGAGGATGGATGGTGATCTTTGGGAGAAAGTTCTTAACCCTGATAATGCCTACAGAAGGCAACTTATTGATCAGGTTGTATCTACAGCT

upper sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 23

gtatgtaataatttttattgttgtgacttgtgacacctgtttcaagatgtccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA
             | | || |  | ||||  || |  | ||    | |   | || |||| |  ||||   ||  |  ||  || | ||    |||  |||   |||||||| || ||||| |||||||||||||| |||||||| |||||  |     | ||||| |||||||| || || ||||||||||| || || ||||| 
------------gtattttatcattacttacgaaaattctt----gttactctca-caatgg--tgac--tttgtagtttgttaatacacaagttttcaattgtagGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGAAAACAATGATTATAGAAGACAGCTTATTGACCAAGTTGTGTCTACTGCT

upper sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 23

gtatgtaataatttttattgttgtgacttgtgacacctgt-ttcaagatgtccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA
        |  ||| |  || ||    ||  ||   || |  |  | ||     |  ||  | | |   ||| ||    ||  | || |  || |||    |   || |||||||| || || ||||||| ||| || ||||| |||||||||   ||||| || || |||||||||||||| ||||| ||||| || || ||||| 
------gtttgtttatcatgctgatggttaagaggtctttgcttcacataaagcctgcagatttttattgaccta----ttattttttcccttttttttgttattagATATGTGGTGGAAAGGATGGATGCTGACCTCTGGGAGAAAGTTCTTAGTCCCGATAACGAGTATAGAAGGCAACTAATTGATCAAGTTGTATCTACTGCT

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), 30 (downstream exon)
Score: 194

GGGATCCTACACTTGCTGTTGTTGCTTACAGACGTGGGCAGTGTGACTATGAACTTATTAACGTCACTAACAAGAATTCGTTATTCAAGCTGCAAGCTAGgtatgtaata ... aaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA

Block sizes: 49 (upstream exon), 28 (downstream exon)
Score: 150

Block sizes: 49 (upstream exon), 29 (downstream exon)
Score: 108

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 246

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA

                 gacttac  putative branch site (score: 246)
                           ttcatattgcatttat  TA-rich tract

Data associated with selected splice site

Sequence

Basic information

Orthologous splice sites

RNA-Seq data