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

gtgcttcttcattgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaattagtgtactgttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG

Basic information

species	Zea mays
transcript	GRMZM2G091151_T02
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g24250.1 (Oryza sativa), 3'ss of exon 2

gtgcttcttcattgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaattagtgtactgttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
|||||| |  || |   |  |  ||| | |  | ||     ||| |      || |  |||  |  | ||| |||| ||    ||||||||| || |  ||||||||||  |||||||| |  || ||||||||||||||||| ||||||||||||||||||||||||||||||
gtgcttttctatcgtcgcccatgtta-actctagtaa----tga-gctcagagctatgcagttttttgattggtgtgct---ttggcagGTTTACAACAGAGCAGGTTCGTAATCTTGATAGGAACAAGCAGTGGTCTAGAGCTCTTGATGGCTCCAATTATCTACCTGGAATG

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G22190.1 (Glycine max), 3'ss of exon 3

-----gtgcttcttcattgcttctaacattac-atttcaatagcacttgatggctttggcaacacaggct--gctaattagtgtactgttctg---gcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
      || |   |   ||||  |   |     | |||  || |  || |     |     |||    ||  | | |||  |||  |  |||    |||| ||| ||    |  | |||  | | |||||||||||||||||||||||||| || |||||||| || | ||| || |||||||||
attctctgttctctttatgctgttgttaccttgaattctttaactgttaaactactaatatacatgatctaagttcattcatgtggttctctatctgcagATTCGCTGCAAAAGAAGTTGAACAACTTGACAAAAATAAGCAGTGGTCTAGGGCTCTTGATGGTTCTAGTTACCTTCCTGGAATG

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G08500.2 (Glycine max), 3'ss of exon 3

-------gtgcttcttcattgcttctaacattacatttcaatagcacttgatggct--ttggcaacac--aggctgctaattagtgtactgttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
       || ||  ||   |  || | || ||  |||     |    || |   ||  |  |||  |   | | |  |   ||  ||  | |    |||| ||||||    |  | |||  | | |||||||||||||||||||||||||| || |||||||| || | ||| || || ||||||
attctctgttctctttatgttgttgttaccttgaattctttaaatgattaactactaatatgcattatctaagttcattcatatggttatctatctgcagATTCACTGCAAAAGAAGTTGAACAACTTGACAAAAATAAGCAGTGGTCTAGGGCTCTTGATGGTTCTAGTTACCTTCCCGGAATG

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G22350.2 (Arabidopsis thaliana), 3'ss of exon 2

-----gtgcttcttcat----tgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaattagtgtactgttc--tggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
       ||||   |||      |||||  |||    | |||||    |||      ||  |   |   |  ||     |   || || | |  |  |||||| | ||  |  || ||     | |||||||| |||| |||||||||||| || |||||||||||| | ||||| || ||||||
catgatagcttgaacatattactcttctttcatgttttgtcaatttttctttgatttttcagttcctttgtatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G22410.1 (Arabidopsis thaliana), 3'ss of exon 1

-----gtgcttcttcat----tgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaattagtgtactgttc--tggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
      |  || |||||      |||||  |||    | |||||    |||      ||  |   |      ||     |   || || | |  |  |||||| | ||  |  || ||     | |||||||| |||| |||||||||||| || |||||||||||| | ||||| || ||||||
tatttatattttttcatattactcttctttcatgttttctcaatttttctttgatttttcagttcctttttatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G22285.1 (Arabidopsis thaliana), 3'ss of exon 3

-----gtgcttcttcat-tgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaa-----ttagtgtactgttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
       ||||   ||| |   |||    | |  | |    |    ||  | | |||  ||   |    |  | |     |  ||||  |    |  |||||| | ||  |  || ||     | |||||||| |||| |||||||||||| || |||||||||||| | ||||| || ||||||
cttgatagcttgaacatattactcttctttcatgtcttgtcaaattttctttgattttacagttcctttttatgaaggcttcggtgttatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG

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|211066153|gb|FL067272.1|FL067272

EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG

EST: gi|211066159|gb|FL067278.1|FL067278

EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG

EST: gi|211068890|gb|FL067279.1|FL067279

EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTC-CTAAAGGAGCAGGTTCTAAATCTTGACAAAAAATAAGCA
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAA-GGAGCAGGTTCTAAATCTTGACAAAAA-TAAGCA

EST: gi|211068893|gb|FL067282.1|FL067282

EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTC-CTAAAGGAGCAGGTTCTAAATCTTGACAAAAAATAAGCA
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAA-GGAGCAGGTTCTAAATCTTGACAAAAA-TAAGCA

EST: gi|211066145|gb|FL067264.1|FL067264

EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG

EST: gi|211066152|gb|FL067271.1|FL067271

EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG

EST: gi|211066151|gb|FL067270.1|FL067270

EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG

EST: gi|211066150|gb|FL067269.1|FL067269

EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG

EST: gi|211066157|gb|FL067276.1|FL067276

EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GGTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGNGGTCTAN
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG

EST: gi|211066156|gb|FL067275.1|FL067275

EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG

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: 151

TGTTCATTAATCTTCAAACTGAGAAGGCTTACTGTCTTCCTGATGGATATGAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 70

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 57

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 78

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tagcacttgatggctttggcaacacaggctgctaattagtgtactgttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG

                             tgctaat  putative branch site (score: 78)
                                           ctgttct  putative PPT
                                taattagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttcttcattgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaattagtgtactgttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA