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

...tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA

Basic information

species	Zea mays
transcript	GRMZM2G451882_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2

tggctctcttgcttgtttggcgttttat--tttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctcta-----tctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
       ||||| ||||      | ||    | ||| | | |  |    |||   | | | |    |||| ||  | | |  |  | ||        | | ||||||||||||||||||||| |||||| ||||||||||||||||||| |||||||||||||||||||||||||||||||| 
------ccttgcgtgttcattactgtaaagctcaacatgtgagaaggtgaattgcgtcttttgttcttct-gtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG

upper sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 2

tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaataatgacctatcacattc-tagttgtaaataatctctctat-ctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
    |   | |  | ||     |  ||| ||||  | ||||     || |        |   ||||  | ||| |   | || | |  || | |   |||||||| |||||||||||  | ||| |||| ||||||||||  || || ||||||||||| || |||||||||||||| 
--tgttattagggtattaacactaatatgttaatctgttaaagcttaatttgctgatcaatgcatttgttgtttttcttcatttattcataccaatttgcagTGTAATTGTTGAAGCCCTGAAGGTGGACAGTCTGCAGAAACTTTGTTCATCACTGGAGCCTATTCTTCGTAGAGTT

upper sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3

---tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctctatctaccct--gcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
    || | | || ||| ||     || || || | | || |  |  | || | || |  |||       |   | ||| | ||   |  |  |||  |  ||||||| ||||| |||||| | ||| |||| ||| |||||| ||| ||||||||  | ||||| |||||||||||||| 
atagggttttatttcttattaa---ttataattcatc-tagttgtttctaatttat-atttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT

upper sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2

--tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
   |    | ||  || ||     |  || |  | | || |  |  | || | || |  |||       |   | ||| | ||   |  |  ||   |||||||| ||||| |||||| | ||| |||| ||| |||||| ||| ||||||||  | ||||| |||||||||||||| 
aaagaagattttatttcttattaatcataatccatc-tacttgtttctaatttat-atttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT

upper sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 2

---------------------------------------tggctctcttgcttgtttggcgttttattttaa--cgtattaataacaaaataatgacctatcacatt--ctagttgtaaat------aatctctctatctacc-ctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
                                       |       ||| |   |  |   || ||||  |   |||| ||| | ||||   |        | |||   |   |||  ||      ||  | | ||| |     |||||||| ||||| ||||| || |||||||||||| | |||||||| || || ||  ||||||| ||||||||  |||| 
gtaatttgtgttgatgcttgtaatttttctgattattgattatggcgttgttgaatctgtaattgatttgtagttgtatgaatgaaaaaagggttgttatgtatattgattgtctgtggatttgagaaagttgtgtatgtgttattgcagTGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGGCTTTGTTCTTCTTTGGAACCGATTCTTCGCCGAGTG

upper sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1

tggctctcttgcttgtttggcgt---tttattttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
     | ||||| |||||    |     | | | ||||| | |||   | | | ||    |||  || |     | ||  |||    | ||| || | |||||||| || || |||||| | ||| |||||||||||||||  || ||||||||  ||||||| |||||||||||||| 
-tttgcccttgcctgtttctattaaacctctatgaacgtctcaatttaacacttatt-tttatgtcagttctaatatag-taaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT

upper sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 1

------tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaata-atgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
        |   ||  |   ||  ||  |||| | |||    |||| |  |    |  ||| ||| |   ||| |  ||||   | |  | |   | |    |||||||| || ||||||||| | ||| |||||||||||||||  || ||||||||| ||||||| |||||||| ||||| 
caaacaaaggaatcgaggcagtg-ggttttttgtattatta-attagttccgttttctatgccctgtt--attttgtttgt---tgaaatgtacttttgttttgcagTGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTT

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|211076796|gb|FL055833.1|FL055833

EST:     GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAG                         TGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC

EST: gi|148941980|gb|EC886967.2|EC886967

EST:     GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAG                         TGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC

EST: gi|211079522|gb|FL055834.1|FL055834

EST:     GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAG                         TGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC

EST: gi|149013593|gb|EE043063.2|EE043063

EST:     GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAG                         TGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC

EST: gi|211076795|gb|FL055832.1|FL055832

EST:     GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAG                         TGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC

EST: gi|71771244|gb|DR969181.1|DR969181

EST:     GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAG                         TGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC

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: 267

TGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGACGCCGGCGGGGGCGCCGGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 189

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 223

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 162

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aaaataatgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA

                                   tctctctatctaccct  CT-rich tract
                      tagttgtaaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacattc