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

...ttttgttcacaagaacaatggatttgaattctgaatacctgttatgcatgttgtgtgataataatttagatcataccttgttctatggtgtcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA

Basic information

species	Zea mays
transcript	GRMZM2G090172_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G090172_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1

ttttgttcacaagaacaatggatttgaattctgaatacctgttatgcatgttgtgtgata-ataatttagatcataccttgttctatggtgtcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA
  || ||     | |         | |    |   | | |      ||  |   || ||  ||   ||  ||  |    ||| ||  |      ||||||||||||||||||||||| ||||| ||||| || || || ||||||||||||||||||||||| || ||||||||||| |||||||||||||||||||||||
-attcttttttgggatttcaagcctcatgagtagctgcatacagaacaaatctagtaattcatttattgaattctttactgtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA

upper sequence: GRMZM2G090172_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G22600.1 (Glycine max), 3'ss of exon 1

ttttgttcacaaga-acaatggatttgaatt--ctgaatacctgttatgcatgttgtgtgataataatttagatcataccttgttctatggtgtcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA
 |   ||||  ||  | | || |  |   |    | || | || | | | || |  |   |     ||||  |   |||  |  |  ||  ||    |||||||||| || || || ||  |  |  |||| || ||  | ||||||||||| ||||| ||||||||||| |||||||| |||||||| ||||| ||||||||
-tgccttcatcagtcatattgcaactatttcaattaaacagctttgaaggatttaatagaacttagatttgaaatttactcttcttaat--tggtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA

upper sequence: GRMZM2G090172_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G35000.1 (Glycine max), 3'ss of exon 1

--ttttgttcacaagaacaatggatttgaattctgaatacctgttatgcatgttgtg--tgataataatttagatcataccttgttctatggtgtcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA
    || |     |      |    ||   || | | |   | || |  |  ||||   ||  |   || | | ||| || || ||      ||| |   | |||||| || ||||| ||  |  | ||||| || ||  | ||||||||||| ||||| ||||||||||| |||||||| ||||||||||||||||| || ||
taacttatcattgattgtgttcatcttttgttgtaactttttttttttaaatttgtaattggcacctatcttg-tcaaactttttttgtctatgtat---gtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTA

upper sequence: GRMZM2G090172_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G04710.1 (Glycine max), 3'ss of exon 1

ttttgttcacaagaacaatggatttgaattctgaatacctgttatgcatgttgtgtgataataatttagatcataccttgtt-----ctatggtgtct-tctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA
  || |     |      |    ||  ||| | | | | | || |     ||||    |  ||||||  | | || ||||||      | |||| | | |  |||||||| || || || ||  |  | ||||| || ||  | ||||||||||| ||||| ||||||||||| ||||| || ||||||||||||||||| || ||
-cttatcactgattgtgttcatcttttattgtaacttctttttttt----ttgtaaatttgtaatttgcacc-tatcttgttaaaatttttggtctatgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTA

upper sequence: GRMZM2G090172_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G24950.1 (Glycine max), 3'ss of exon 1

-ttttgttcacaaga-acaatggatttgaattctgaatacctgttatgcatgttgtgtgataataatttagatcataccttgttctatggtgtcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA
 ||   ||||  ||  |   |   | |      | || | || | | | || |  |   |     ||||  |   |||  |  |  ||  ||    |||||||||| || || || ||  |  | ||||| || ||  | ||||||||||| ||||| ||||||||||| |||||||| |||||||||||||||||||||||
attgccttcatcagtcattgtaagtatttcaattaaacagctttgaaggatttaatagaacttagatttgaaatttactcttcttaat--tggtccctgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGACATATA

upper sequence: GRMZM2G090172_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT1G70660.2 (Arabidopsis thaliana), 3'ss of exon 1

-------------------------------------------------------------ttttgttcacaagaacaatggatttgaattctgaatacctgttatgcatgttgtgtgataataattta--------gatcata-----ccttgttctatggtgtct--tctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA
                                                             |||  || |      |  | | ||| || |    ||     |||  ||  ||| |   | |   | ||        ||||||      | ||| |  ||  ||| |  | |||||||||||||||||||||  |  | ||||| |||||| | |||||||| || ||||| ||||| || ||||| ||||| ||||||||||||||||| || | 
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacgattttgattacacagattgcgaagtcactctatatcgttgttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT

upper sequence: GRMZM2G090172_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1

ttttgttcacaagaacaatggatttgaattc-tgaatacctgttatgcatgttgtgtgataataatttagatcataccttgttctatggtgtcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA
   |||  |   || | ||||  | || |   |  ||| ||| | || |   ||  |     |      |||  |     |  ||    | | |  || |||||| || ||||||||  || | ||||| || ||| | |||||||| || ||||| ||||| ||||| |||||||| ||||||||||||||||| || ||
gaatgtg-atcggatccatggtctcgattaggtatatatctgatctgtaaaatgatttgatttgggggcgatatttataagagcttgattttgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA

upper sequence: GRMZM2G090172_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 1

ttttgttcacaagaacaatggatttgaattctgaatacctgttatgcatgttgtgtgataataatttagatcataccttgtt--ctatggtgtcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA
|| | ||   ||      ||| | |   | ||  ||     || ||  || | ||     |||         ||| |||  |   | ||  ||| | ||||||||| || || || ||  | || ||||| || ||  | || || ||||| ||||| ||||||||||| || ||||| ||||||||||||||||| |||||
ttatcttggaaaattttctggttgttgttgctacatggtcttt-tgagtgct-tgcatgcatagcaggagatatatctttgtgattttgtggtcatatgcagTTCCAAGGAATTTCAGATTACTGGAAGAGCTTGAGAGAGGGGAAAAGGGAATTGGCGATGGAACTGTCAGTTATGGAATGGATGATGCTGATGATATATA

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|211187615|gb|FL186093.1|FL186093

EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA

EST: gi|211185215|gb|FL186078.1|FL186078

EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA

EST: gi|211185214|gb|FL186077.1|FL186077

EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA

EST: gi|211187617|gb|FL186095.1|FL186095

EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA

EST: gi|32788418|gb|CD940654.1|CD940654

EST:     GATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: GATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA

EST: gi|211187616|gb|FL186094.1|FL186094

EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA

EST: gi|211185223|gb|FL186086.1|FL186086

EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA

EST: gi|211187612|gb|FL186090.1|FL186090

EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA

EST: gi|31558072|gb|CD527284.1|CD527284

EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA

EST: gi|211185219|gb|FL186082.1|FL186082

EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA

EST: gi|211185221|gb|FL186084.1|FL186084

EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAANGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA

EST: gi|71438019|gb|DR819069.1|DR819069

EST:     AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCG                         TTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA
genomic: AGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCA

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), 45 (downstream exon)
Score: 60

TCGTCTCCCGTCTCGAGAGATTGCAGGGGGCGGCGCTCGAAGCTGGAGGAAGCGGACGGGTTCGCGATGGGGTCCGAGGGATCCTCGGGTCCGGTCGTCGgtgagtagca ... tcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 76

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 71

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 40

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gcatgttgtgtgataataatttagatcataccttgttctatggtgtcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA

                                           tgtcttct  CT-rich tract
            ataataatttagatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgttcacaagaacaatggatttgaattctgaatacctgttatgcatgttgtgtgataataatttagatcataccttgttctatggtgtcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
ttttgtt
- - - - - aagaaca
- - - - - - - - - - - - - - - - - atacctg
- - - - - - - - - - - - - - - - - - - - - - tgcatgt