ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...tttgctttttgaagaggaaagacatcctgctattacctctctgtctgcccatttgggacttttcagatatcccttaacttgtaatctacacctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGCAATCTGCCAAGTGGACCAAGAGCCATTCGAAGGTTTAATGACGGACAAT

Basic information

species	Zea mays
transcript	GRMZM2G006429_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G006429_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g18970.1 (Oryza sativa), 3'ss of exon 6

----tttgctttttgaagaggaaagacatcctgctattacctctctgtctgcccatttgggacttttcagatatcccttaacttgtaatctacacctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGCAATCTGCCAAGTGGACCAAGAGCCATTCGAAGGTTTAATGACGGACAAT
    | | || ||||  ||||||   ||  ||| | |||||||   ||||   |||||| | || || |      |||||||     || || || ||| |||||||||| || ||||||||| ||||||||||   | | |||| |||||||||||||||||||||||| ||||  || || |||| |||| |||| || |||
ttgatgttctgtttgtcgaggaagcccactctgttgttacctc---gtctctgcatttgaggctattgaacagaaccttaacagcctatttatactttt-gcagGTTGGGTAGGAATTTTCCATCAAAAGCAAACTCGTCCCCATCTCGCTGTGCAATCTGCCAAGTGGATCAAGCACCTTTTGAAGATTTAGTGACAGATAAT

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|71759367|gb|DR957304.1|DR957304

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|5688654|gb|AI941669.1|AI941669

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|50331893|gb|CO527019.1|CO527019

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|101394555|gb|EB819212.1|EB819212

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|78543568|gb|DV621066.1|DV621066

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|211160527|gb|FL223273.1|FL223273

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTKTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|148940664|gb|EC885476.2|EC885476

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|71762481|gb|DR960418.1|DR960418

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|166509825|gb|EG259139.1|EG259139

EST:     TGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGA-GAAAG                         GTTGGGAAGTAATTTTCCACCAA
genomic: TGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAA

EST: gi|22521667|gb|BU080478.1|BU080478

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|71331540|gb|DR802615.1|DR802615

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|74233457|gb|DT641371.1|DT641371

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|78123110|gb|DV541494.1|DV541494

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|67021571|gb|CO450320.1|CO450320

EST:     GGCTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|21891454|gb|BQ744667.1|BQ744667

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCCCCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|19769571|gb|BQ034292.1|BQ034292

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|32807330|gb|CD959564.1|CD959564

EST:     GATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|67022466|gb|CO451215.1|CO451215

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|149108126|gb|EE292475.2|EE292475

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

EST: gi|24769233|gb|CA404362.1|CA404362

EST:     GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAG                         GTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC
genomic: GGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGC

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), 48 (downstream exon)
Score: 240

GTAAAAGGTCTCATAGTTCTGTTGGAAAGCTCAGCAAATCTGCTTCATTGGGTTCAGTGGAAGAAATATTCGAGGAGGGATCTGCAATGTTGGAAGAAAGgcatgttctt ... cctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGCAATCTGCCAAGTGGACCAAGAGCCATTCGAAGGTTTAATGACGGACAAT

Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 34

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 57

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 82

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgcccatttgggacttttcagatatcccttaacttgtaatctacacctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGCAATCTGCCAAGTGGACCAAGAGCCATTCGAAGGTTTAATGACGGACAAT

                          ccttaac  putative branch site (score: 82)
                                           cacctttc  putative PPT
                            ttaactt  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgctttttgaagaggaaagacatcctgctattacctctctgtctgcccatttgggacttttcagatatcccttaacttgtaatctacacctttcgcagGTTGGGAAGTAATTTTCCACCAAAAGCAAATCTGCCTCCATTTCGCTGTGCAATCTGCCAAGTGGACCAAGAGCCATTCGAAGGTTTAATGACGGACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
tttgctt
- - - - - - - - -aaagaca
- - - - - - - - - - - - -cctgcta
- - - - - - - - - - - - - - - - - - - - -tgtctgc
- - - - - - - - - - - - - - - - - - - - - - - - ccatttg