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

...tcaatgattgtgccatatcttcagtggcttcttgttattgccgtgcctccttttatatgacagataacgttactgctctacctccttttatatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTATAGTGGAGATGATCTGACAAACGTTTGCCGCGATGCCTCAATGAATGGCA

Basic information

species	Zea mays
transcript	GRMZM2G017305_T02
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G017305_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 6

-tcaatgattgtgccatatcttcagtggcttcttgttattgccgtgcctccttttatatgacagataacgttactgctctac-ctccttttatatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTATAGTGGAGATGATCTGACAAACGTTTGCCGCGATGCCTCAATGAATGGCA
    |  ||      |||   |  |   ||| |  |  |||  |       |  | |   | |  |   |||  |  |  || |  |||||||||| | ||| | ||  | |||||| |||| || || ||||| ||||||||||||||||||||||| || || || ||||| |||||||| ||||| |||||||||||||
cgtgaaaatgaccaaatactgttcgctacttgtcatctttgatgaaaaag-tactgtgccatatcttctgttgtttgttaacgcctcttttatatc-ggcagGTTGCTACCGATGTTGACATAGATGAAGTTGCACGGAGGACAGAAGGCTATAGTGGTGACGACCTTACAAATGTTTGCCGTGATGCTTCAATGAATGGCA

upper sequence: GRMZM2G017305_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 6

--tcaatgattgtgccatatcttcagtggcttcttgttattgccgtgcctccttttatatgacagataacgttactgctctacctccttttatatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTATAGTGGAGATGATCTGACAAACGTTTGCCGCGATGCCTCAATGAATGGCA
  |    ||       ||       |  ||    |  |  |||     ||    |||| |||    |    ||| ||||     | ||| | | |    ||| | ||  | ||||| || || ||||| || |||||  ||||||| || ||||||||||||||| ||||||| || || |||||||| ||  ||||||| |
actgtgagaacagtttatggaaagggcagcagaataatgatgctaaaacttggattat-tgattattgttattattgctgattgtacttgtct-ttcaccagGTGGCACCTGATGTCAATATAGACGAAGTGGCTCGCCGGACAGAGGGATATAGTGGAGATGATTTGACAAATGTCTGTCGCGATGCTTCCTTGAATGGTA

upper sequence: GRMZM2G017305_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G22210.1 (Glycine max), 3'ss of exon 6

tcaatgattgtgccatatcttcag--tggcttcttgttattgccgtgcctccttttatatgacagataacgttactgctctacctccttttatatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTATAGTGGAGATGATCTGACAAACGTTTGCCGCGATGCCTCAATGAATGGCA
||| | | |   |  ||   | ||    | || | |  |  || |      | |     | | |  ||   ||| ||||     | ||| | | |    ||| | ||  | ||||| || || ||||| || |||||  ||||||| || ||||||||||||||| ||||||| || || |||||||| ||  ||||||| |
tcagtcactaaact-tactgtgagaacagtttatggaaagggcagcagaatcatgatgctaaaacttattattattgctgattgtacttgtct-ttcaccagGTGGCACCTGATGTCAATATAGACGAAGTGGCTCGCCGGACAGAGGGATATAGTGGAGATGATTTGACAAATGTCTGTCGCGATGCTTCCTTGAATGGTA

upper sequence: GRMZM2G017305_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 6

----tcaatgattgtgccatatcttcagtggcttcttgttattgccgtgcctccttttatatgacagataacgttactgctctacctccttttatatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTATAGTGGAGATGATCTGACAAACGTTTGCCGCGATGCCTCAATGAATGGCA
    ||| ||||| |  | ||  |    |  |       || ||   | |  | | |||    | | ||  | ||| ||   |      ||    ||||  ||| | ||  | ||||| || |||||||| || |||||  | || || || || |||||||||||||||||||| |||||||| ||||| ||  | |||||||
ttgctcattgattttaacctacttgacttaacaatcatgtactgt-atactccttattaagctagatatgtctttattgggttgttgtatt---catctatcagGTGGCTCCTGATGTAAATATCGACGAAGTGGCTCGCCGCACTGAGGGGTACAGTGGAGATGATCTGACAAATGTTTGCCGGGATGCTTCCTTAAATGGCA

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|28985682|gb|CB350761.1|CB350761

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|211478494|gb|FL368092.1|FL368092

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|67021540|gb|CO450289.1|CO450289

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|18174356|gb|BM349744.1|BM349744

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|5055466|gb|AI734353.1|AI734353

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|67015406|gb|CO444155.1|CO444155

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|28984876|gb|BQ539249.2|BQ539249

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|24767871|gb|CA403006.1|CA403006

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|211038213|gb|FL329861.1|FL329861

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|78024488|gb|DV492875.1|DV492875

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|31360569|gb|CD444926.1|CD444926

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|16378018|gb|BI992248.1|BI992248

EST:     ATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|213192745|gb|FM193924.1|FM193924

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGANNNNNTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|17929404|gb|BM266364.1|BM266364

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|61119244|gb|DN560205.1|DN560205

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAC
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|60344133|gb|DN211106.1|DN211106

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

EST: gi|20301545|gb|BQ164488.1|BQ164488

EST:     ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG                         ATAGCCGCAGATGTTAACATCGACGAGGTTGCTCTGTGGACATATGGCTAT
genomic: ATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTAT

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: 48 (upstream exon), 47 (downstream exon)
Score: 97

GCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAGgtatgtattg ... tatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTATAGTGGAGATGATCTGACAAACGTTTGCCGCGATGCCTCAATGAATGGCA

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 26

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 51

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 67

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cctccttttatatgacagataacgttactgctctacctccttttatatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTATAGTGGAGATGATCTGACAAACGTTTGCCGCGATGCCTCAATGAATGGCA

                agataac  putative branch site (score: 67)
                              ctctacctccttttat  putative PPT
     ttttatatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaatgattgtgccatatcttcagtggcttcttgttattgccgtgcctccttttatatgacagataacgttactgctctacctccttttatatctgacagATAGCCGCAGATGTTAACATCGACGAGGTTGCTCGGAGGACAGAAGGCTATAGTGGAGATGATCTGACAAACGTTTGCCGCGATGCCTCAATGAATGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- -atgattg
- - - - - tgccata
- - - - - - - - - - - - -ggcttct
- - - - - - - - - - - - - - - - - - - - - -tgcctcc