ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaacaattctcatggagaaattgtttaatgatatcctgatttcttaatctgatcatctgtgcaattaaattgcag

Basic information

species	Zea mays
transcript	GRMZM2G078756_T01
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G078756_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 9

TAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgt-acatgcaacaattctcatggagaaattgtttaatgatat-cctgatttcttaatctgatcatctgtgcaattaaattgcag
 |||||||||||||||||||| ||||| || ||||||||||| ||||| |||||||||||||||||||| || || || |||||||| ||| |  | ||||| |||| | || |     |||       | ||  ||||||| |||   || |||  |||| ||| | | |||||   ||||||
CAATTTCACCAACAAGAAAGGAATGACGAGCCATTGCTACAGGATAGCCTATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcgacgacatctatga------ttttagatgatattccttggtttttatactgaacatgtctacaatttggttgcag

upper sequence: GRMZM2G078756_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G10060.1 (Glycine max), 5'ss of exon 9

TAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtac---atgcaac----aattctcatggagaaattgtttaatgatatcctgatttctta-atctgatcatctgtgcaattaaattgcag--------------------
 || ||||||||||||||||| ||||| || || ||||| || || ||||||||||| ||||||||||| ||||| || ||||| || ||| |||| ||||||    ||  ||     ||| ||  || |   ||   |     |  ||||   || | | || |  |  |    |  |  ||                           
CAACTTCACCAACAAGAAAGGAATGACCAGCCACTGCTATAGGATTGCATATAGGTCTATGGAACGTTCTCTCACTGATGAGGAAATAAACGATCTGCAGgtattaaatataattagaaatactagtgcaatcataactagtctaggtcctatgttgtcatattttgttttgaaagttaccaacacttgtttttccccttgtcaatgcag

upper sequence: GRMZM2G078756_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA18G52890.1 (Glycine max), 5'ss of exon 11

TAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaacaattctcatggagaaattgtttaatgatatcct-gatttcttaatctgatcatctgtgcaattaaattgcag---------------------------
 |||||||||||||||||||| ||||| || || ||||| || || ||||||||||| ||||||||||| ||||| || ||||| || ||| |||| ||||||      |  |||   ||           | | |  ||  || | | |  |  | | ||  | |||      |  |  ||                            
CAATTTCACCAACAAGAAAGGAATGACCAGCCACTGCTATAGGATTGCATATAGGTCTATGGAACGTTCACTCACTGATGAGGAAATAAACGATCTGCAGgtattaaatattattagaattactggtgcaatcattactagtctaggtcttatgttgtcatattttgttttgaaagttaccaacacttgttttaccccttgtcaatgcag

upper sequence: GRMZM2G078756_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 5'ss of exon 9

TAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgta---catgcaacaattctcatggagaaattgttta-atgatatcctgatttct--taat--ctgatcatctgtgcaattaaattgcag------------
 |||||||||||||||||||| ||||| ||||| || ||  | ||||||||  |||| ||||| ||||| || ||||| |||||||| ||  |  | ||||||   ||||    |    |  || | || |  ||   ||  | || ||||| ||  ||||  ||||| | |||   ||||    |                
CAATTTCACCAACAAGAAAGGAATGACCAGTCAATGTTATCGGATAGCATACCGGTCCATGGAGCGTTCACTTACAGATGAGGAGATAAATGAGTTGCAGgtatgtcatgtttaagggattttgtacaagtaattagtattttgtcttgattgctggtaataactgataacctgg--aatttggctatgattctgggtgtag

upper sequence: GRMZM2G078756_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv19s0027g01480.t01 (Vitis vinifera), 5'ss of exon 4

TAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacat-gcaacaattctcatggagaaattgtttaatgat--atcctgatttct--taat--ctgatcatctg----tgcaattaaattgcag------
 |||||||||||||||||||| ||||| ||||| || ||  | ||||||||  |||| ||||| ||||| || ||||| |||||||| ||| |  | ||||||  |       |      | |   || || ||| |  |   || ||||| |   ||||  || || | |||    |    ||  |||   |      
CAATTTCACCAACAAGAAAGGAATGACCAGTCAATGTTATCGGATAGCATACCGGTCCATGGAGCGTTCACTTACAGATGAGGAGATAAACGAGTTGCAGgtatttcatgtttaggggatttgtacaagtgattagtatttcgtcttgattacgggtaatgactaataacctgaaatttggctttgattctgggtgcag

upper sequence: GRMZM2G078756_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 5'ss of exon 9

TAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgta---catgcaacaattctcatggagaaattgttta-atgatatcctgatttcttaatctgatcatctg--tgcaattaaattgcag-------------
 |||||||||||||| ||||| ||||| ||||| || ||  | ||||||||  |||| ||||| ||||| || ||||| |||||||| ||  |  | ||||||   ||||         |  || | || |  || | ||    || ||||| |      |||  |      || ||||    |                 
CAATTTCACCAACAACAAAGGAATGACCAGTCAATGTTATCGGATAGCATACCGGTCCATGGAGCGTTCACTTACAGATGAGGAGATAAATGAGTTGCAGgtatttcatgtttaggggattttgtacaagtgattaatatttcgtcttgattacaggtaatgactaataacctggaatttggctatgattctggggtgcag

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|32856608|gb|CD996289.1|CD996289

EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG

EST: gi|211308521|gb|FL467499.1|FL467499

EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG

EST: gi|76910024|gb|DV163657.1|DV163657

EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG

EST: gi|31072245|gb|BQ479053.1|BQ479053

EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG

EST: gi|78113854|gb|DV532243.1|DV532243

EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG

EST: gi|71762613|gb|DR960550.1|DR960550

EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG

EST: gi|78079223|gb|DV507635.1|DV507635

EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG

EST: gi|60395362|gb|DN228231.1|DN228231

EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG

EST: gi|71310636|gb|DR791614.1|DR791614

EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG

EST: gi|211026939|gb|FL261356.1|FL261356

EST:     ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAG                         TTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG
genomic: ATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAG

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: 195

TAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaa ... taaattgcagTTGAATGTCAGGGAAGCTGTGAAAGATAAATTGAAAGTAGAGTTGAGATAGCAGCAGCTAATTATGCTGTCATAGCATGGACTAAATTTTGCCTGTCTTT

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 227

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 143

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgtacatgcaacaattctcatggagaaattgtttaatgatatcctgatttcttaatctgatcatctgtgcaattaaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT