ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTGTTCGGGCCATAGTGCCGAGAATGAATCTGGACGATCTCTTTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaaagcctttttttactggtaggggattggctcgatatcattggttctgcttgtaactgcagtgacacatctggtcattctcttggtgataat...

Basic information

species	Zea mays
transcript	GRMZM2G173858_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G173858_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g04460.1 (Oryza sativa), 5'ss of exon 3

TTGTTCGGGCCATAGTGCCGAGAATGAATCTGGACGATCTCTTTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaaagccttt--ttttactggtaggggattggctcgatatcattggttctgcttgtaactgcagtgac-acatctggtcattctcttggtgataat
| || || || ||||| |||||||||||||| || ||||| |||||||| ||||| |||||||| ||||||||| |  ||||||| |||||||||    ||   |  ||   || |    |  |   |         |  ||   |        ||  |   ||  | |||| |  |  ||   |   |  |   
TGGTCCGAGCTATAGTTCCGAGAATGAATCTTGATGATCTTTTTGAGCAAAAGAATGATGTGGCGAAAGCTGTACTTCAGGAGCTAGAAAAGgtaaccgtatgccaattaacttgatcttttagttgtgaaaattccagtatacatctaatcaatattttaggtttctacatgtattgcttgcttctattgt---

upper sequence: GRMZM2G173858_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 3

TTGTTCGGGCCATAGTGCCGAGAATGAATCTGGACGATCTCTTTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaaagcctttttttactggtaggggattggctcgatatcattggttctgcttgtaac-tgcagtgacacatctggtcattctcttggtgataat----
|   ||| || || || |||||||||||  ||||||| || ||||||||||||   || || ||||||||||| |||||||| ||||||||||||| |      | | ||||   |      |   ||||    |   |||   | ||   | ||  || || ||  | |    | | | | ||| | | ||     
TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatctt----acttcttttatttaagtaagttctggcattcttgaattaaatatgtaagaaaagtgaagagaagcttagtattagt-tgttgttcacaaaatat

upper sequence: GRMZM2G173858_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G28170.1 (Glycine max), 5'ss of exon 3

TTGTTCGGGCCATAGTGCCGAGAATGAATCTGGACGATCTCTTTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaaagcctttttttactggtaggggattggctcgatatcattggt---tctgcttgtaactgcagtgacacatctggtcattctcttggtgataat--
|   ||| || || || || ||||||||  |||| || |||||||||||||||   || || ||||||||||| |||||||| ||||||||||||  |    |   || ||| | |  | | |   |   |  | |     |     | |  ||||      | |  || ||    |||||  |||  | | | |  
TGACTCGTGCTATTGTTCCTAGAATGAACTTGGATGAACTCTTTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtaact----acttttatttaagttctggcgttctttatgaaaagtgaagagaagtttagttgttcacaaaatatcaaattatttcatttccttt-taaaactat

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|211063146|gb|FL170413.1|FL170413

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCAT
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCAT

EST: gi|93011732|gb|EB637252.1|EB637252

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|78092689|gb|DV521063.1|DV521063

EST:     ACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATGGAGCACATTCTCATGGTTGATATC
genomic: ACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|76290522|gb|DV030090.1|DV030090

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|50337496|gb|CO532622.1|CO532622

EST:     AGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: AGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|149064913|gb|EE286585.2|EE286585

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|67017254|gb|CO446003.1|CO446003

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|74235256|gb|DT643170.1|DT643170

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|149076480|gb|EE165106.2|EE165106

EST:     GCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: GCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|149076481|gb|EE165107.2|EE165107

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|71444069|gb|DR825119.1|DR825119

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|78115187|gb|DV533575.1|DV533575

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|71420003|gb|DR804972.1|DR804972

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|149089179|gb|EE178367.2|EE178367

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|89251645|gb|DY623431.1|DY623431

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|71766674|gb|DR964611.1|DR964611

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|149075337|gb|EE163844.2|EE163844

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|76921437|gb|DV168585.1|DV168585

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|149064912|gb|EE286584.2|EE286584

EST:     GAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: GAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|71419996|gb|DR804971.1|DR804971

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|211060193|gb|FL170400.1|FL170400

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|211063148|gb|FL170415.1|FL170415

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGGTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|148969751|gb|EE020628.2|EE020628

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|71762921|gb|DR960858.1|DR960858

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

EST: gi|101385178|gb|EB814635.1|EB814635

EST:     TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAG                         GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC
genomic: TTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATC

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), 47 (downstream exon)
Score: 97

TTGTTCGGGCCATAGTGCCGAGAATGAATCTGGACGATCTCTTTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaa ... tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAG

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 127

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 188

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTTCGGGCCATAGTGCCGAGAATGAATCTGGACGATCTCTTTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaaagcctttttttactggtaggggattggctcgatatcattggttctgcttgtaactgcagtgacacatctggtcattctcttggtgataat

- - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT