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

...tgcttttattaatgcattgcaattacatcatatgtattgaagattatgtctacattaatattatgttggccctttttcttacttcattacatgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAAT

Basic information

species	Zea mays
transcript	GRMZM2G095670_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G095670_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g55290.1 (Oryza sativa), 3'ss of exon 2

-tgcttttattaatgcattgcaattacatcatatgtattgaagattatgtctacattaatattatgttggccctttttcttacttc-attacatgttcccagGACATTCATTGGAGT----GCTCC-----ATTCATTGAGGCAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAAT
  |  |  ||||     ||  |||  | | |  |  || |||||   || |    | ||| || ||       |   ||||||  | | |  |||| | ||||   |   |   ||     || ||      |||||||||  | ||||||||| |||||||||||||||||||| ||||||| ||||||||||||||||||         
tagtgtccattatgttcttataatctcttgagttcgatggaagagcctgaccgtgtaaatgttttgc--attgtgaatcttacacctactctatgtcctcagGGTTTCTTTGCAAGCTTTAGCCCCTCGACGTTCATTGAGAGAACATGCCTAAAATAAAGACAAGCCGTGTCAAATATCCTGGAGGATGGGAGCTTATTGA---------

upper sequence: GRMZM2G095670_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 1

-tgcttttattaatgcattgcaattacatcatatgtattgaagattatgtctacattaatattatgt----tggccctttttcttacttcattacat----gttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAAT
  |  | |||||     ||  |||  | | |  |  || |||||   || |      ||| |  ||     ||   |||   | ||||  ||  | |    ||| |   |  |    | |  |  |  | ||||||||   | ||||||||| |||||||||||||||||||| ||||||| ||||||||||||||||||         
tagtgtgtattatgttcttataatctcttgagttcgatggaagagcttgaccgtgcaaatgtattgcattgtgaatcttacacctactctatgtcctcagGGTTTCTTTGCAAGCTTTAGCCGCTCGACGTTCATTGACAGAACATGCCTAAAATAAAGACAAGCCGTGTCAAATATCCTGGAGGATGGGAGCTTATTGA---------

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|78543888|gb|DV621386.1|DV621386

EST:     TCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA
genomic: TCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA

EST: gi|60359481|gb|DN226454.1|DN226454

EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA

EST: gi|211218105|gb|FL085264.1|FL085264

EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA

EST: gi|71306037|gb|DR789154.1|DR789154

EST:     GAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA
genomic: GAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA

EST: gi|211218101|gb|FL085260.1|FL085260

EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA

EST: gi|211218104|gb|FL085263.1|FL085263

EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATT-AGGCAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA

EST: gi|211218102|gb|FL085261.1|FL085261

EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGMTAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA

EST: gi|78544043|gb|DV621541.1|DV621541

EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA

EST: gi|60394589|gb|DN227459.1|DN227459

EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA

EST: gi|19822372|gb|BQ048396.1|BQ048396

EST:     GGTGCAGA-TGGAGATCCGCCCGGAC-TGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA

EST: gi|211215545|gb|FL085259.1|FL085259

EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATT-AGGCAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA

EST: gi|211215544|gb|FL085258.1|FL085258

EST:     GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTG                         GACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA
genomic: GGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGA

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: 429

AGGACTTTGTCCCTTTACGTCGTTGTCCAGCTCCTCGCATATTGTGGCCTGGTGCAGATTGGAGATCCGCCCGGACTTGGATCGAGTCCTCCTGTCTTTGgtaaggaaac ... atgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 272

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 191

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 272

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atgtctacattaatattatgttggccctttttcttacttcattacatgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAAT

                              ttcttac  putative branch site (score: 272)
                                              tgttccc  putative PPT
     tacattaatattatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttttattaatgcattgcaattacatcatatgtattgaagattatgtctacattaatattatgttggccctttttcttacttcattacatgttcccagGACATTCATTGGAGTGCTCCATTCATTGAGGCAGCATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATTGAACCAACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
tgctttt
- - - - - -atgcatt
- - - - - - - - - - - - - - -atatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgttg