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

gtcaatatccttataagtgctgtttggttttccactctgaattttatgatcttaactgttttttttgggtccgttgctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACATAGGGAGATCTGATGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGG

Basic information

species	Zea mays
transcript	GRMZM2G063355_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G063355_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g41110.1 (Oryza sativa), 3'ss of exon 3

gtcaatatccttataagtgctgttt-ggttttccac----tctgaattttatgatcttaactgttttttttgggtccgttgctcatgt-tagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACATAGGGAGATCTGATGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGG
||  |  || | | ||    |||||  || || |||    |||   || ||| | || |||||  |||| |   || |||| | |||| ||||||||||||||||||||||||||||||| || || ||||| || ||||| ||||||| | |||| || ||||| ||||| ||||| ||||| || | |||
gttgacctc-tcacaatgcttgtttcagtgtttcacgtgctctcttttgtataagctaaactgccttttgt---tctgttggtaatgtatagCATCAAAGCCAGAAGAGGAGGAAGACATACCATCGATGGATACATTGGATATAGGGAAAACTGAAGGGATAAACTCTATTCCCTCATACTTCAGTGCTGG

upper sequence: GRMZM2G063355_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 3

gtcaatatccttataagtgctgttt-ggttttcc----actctgaattttatgatcttaactgttttttttgggtccgttgctcatgt-tagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACATAGGGAGATCTGATGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGG
||  |  ||     | |   |||||  || || |    |||||   || |||   || ||||   |||| |   || |||| | |||| |||||||||||| |||||||||||||||||| || || ||||| || ||||| ||||||| | |||| || ||||||||||| ||||| || || || | |||
gttgacctctcagaatgccttgtttcagtgtttcgcgcactctcttttgtataggctaaactcccttttgt---tctgttggtaatgtatagCATCAAAGCAAGAAGAGGAGGAAGACATACCATCGATGGATACATTGGATATAGGGAAAACTGAAGGGATAAAGTCTATTCCCTCATATTTCAGTGCTGG

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|211036315|gb|FL466133.1|FL466133

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

EST: gi|33770858|gb|CF273152.1|CF273152

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

EST: gi|211327140|gb|FL012759.1|FL012759

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

EST: gi|211327148|gb|FL012767.1|FL012767

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

EST: gi|211324977|gb|FL012746.1|FL012746

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTT
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTT

EST: gi|211329311|gb|FL012773.1|FL012773

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

EST: gi|211327149|gb|FL012768.1|FL012768

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACN
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGAC-

EST: gi|211327147|gb|FL012766.1|FL012766

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

EST: gi|148971664|gb|EE022387.2|EE022387

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

EST: gi|26559206|gb|CA831441.1|CA831441

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

EST: gi|15208976|gb|BI430860.1|BI430860

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

EST: gi|211329317|gb|FL012779.1|FL012779

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACAC
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACAC

EST: gi|211324974|gb|FL012743.1|FL012743

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

EST: gi|211324988|gb|FL012757.1|FL012757

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCNAG                         CATCAAAGACAGAAGAGGAGGAAGACAT-CCCTCTATGGAC
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGAC

EST: gi|50331765|gb|CO526891.1|CO526891

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

EST: gi|211327141|gb|FL012760.1|FL012760

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAKGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

EST: gi|22542051|gb|BU092489.1|BU092489

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAG                         CATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

EST: gi|211327145|gb|FL012764.1|FL012764

EST:     GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCWACACATGGAGTGCAAG                         CATCAWAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA
genomic: GGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACA

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: 174

AGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACATGGAGTGCAAGgtcaatatcc ... ctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACATAGGGAGATCTGATGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 345

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 242

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 233

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ccactctgaattttatgatcttaactgttttttttgggtccgttgctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACATAGGGAGATCTGATGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGG

                  tcttaac  putative branch site (score: 233)
        aattttatgatcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaatatccttataagtgctgtttggttttccactctgaattttatgatcttaactgttttttttgggtccgttgctcatgttagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACATAGGGAGATCTGATGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA