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

gtacacacctcatttctaatgctgcagtaagttatatcttctgtatgtgtaactgctaatgtattttactgctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAGTGGAAGGAGTCTGAATACTCTGGCCATTCTATTCCTGTTGGTGGTCTTG

Basic information

species	Zea mays
transcript	GRMZM2G130987_T04
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G130987_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 4

gtacacacctcatttctaatgctgcagtaagttatatcttctgtatgtgtaact---gctaatgtattt-tactgctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAGTGGAAGGAGTCTGAATACTCTGGCCATTCTATTCCTGTTGGTGGTCTTG
||    || ||| ||| | ||||  || ||| || |||||   | | |||   |     |||  | ||| || |||| |  |||||||||||||||| |||||||||||| ||||| || |||||| ||||||| |||||||| ||||| ||||||||||||||| ||||||||||||||||||
gtctgaacttcaattccactgctttagcaagataaatctttaatgtttgtgtttagcattaacatgtttgtattgctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG

upper sequence: GRMZM2G130987_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv19s0014g01020.t01 (Vitis vinifera), 3'ss of exon 4

gtacacacctcatttctaatgctgca---gtaagttat----atcttctgtatgtgtaactgctaatgtattttactgctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAGTGGAAGGAGTCTGAATACTC---TGGCCATTCTATTCCTGTTGGTGGTCTTG
      || | |  | |||   || |    | ||||      || ||||    |||| | | ||||   |||||| | ||   |||| | || ||||||| |||||||||||| |||||||| || ||  | || ||||||||||| |||||||| ||   ||| || |  || |||||||||||||   
----gtacttgagctttaagcttgtatacatgagttgcggtcattttcttctggtgtta-tactaaca-attttatttct--tacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAGTGGAAGGAATCTGAATATTCGGGTGGTCAATACATCCCTGTTGGTGGTC---

upper sequence: GRMZM2G130987_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv00s0551g00030.t01 (Vitis vinifera), 3'ss of exon 1

---gtacacacctcatttctaatgctgcagtaagttatatcttctgtatgtgtaactgctaatgtattttactgctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAGTGGAAGGAGTCTGAATACTCTGGC---CATTCTATTCCTGTTGGTGGTCTTG
    |  |    | |  |   || |    ||  |    || ||||    |||| | | ||||   |||||| | ||   |||| | || ||||||| |||||||||||| |||||||| || ||  | || ||||||||||| |||||||| || |||   || |  || |||||||||||||   
gtactggagctttaagcttgtatacacaggttggggtcattttcttctggtgtta-tactaaca-attttatttct--tacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAGTGGAAGGAATCTGAATATTCAGGCGGTCAATACATCCCTGTTGGTGGTC---

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|213167499|gb|FM192311.1|FM192311

EST:     CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|211338837|gb|FL045914.1|FL045914

EST:     CCATCATTCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|31352161|gb|CD436518.1|CD436518

EST:     CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|31352309|gb|CD436666.1|CD436666

EST:     CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|67012434|gb|CO441183.1|CO441183

EST:     CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|13150076|gb|BG320398.1|BG320398

EST:     CCATCATTCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAMGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|13150010|gb|BG320332.1|BG320332

EST:     CCATCATTCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|6526954|gb|AW216197.1|AW216197

EST:     CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|5895581|gb|AW036827.1|AW036827

EST:     CCATCATTCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|61118439|gb|DN559400.1|DN559400

EST:     CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|211338835|gb|FL045912.1|FL045912

EST:     CCATCATTCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|33095855|gb|CF055849.1|CF055849

EST:     CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|60355360|gb|DN222333.1|DN222333

EST:     CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|67024923|gb|CO453672.1|CO453672

EST:     ACCAACCTTTATCTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: ACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|67015216|gb|CO443965.1|CO443965

EST:     CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTTTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|32863571|gb|CF003253.1|CF003253

EST:     CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|31354436|gb|CD438793.1|CD438793

EST:     CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|211341224|gb|FL045920.1|FL045920

EST:     CCATCATTCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|211341223|gb|FL045919.1|FL045919

EST:     CCATCATTCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

EST: gi|92087935|gb|EB484166.1|EB484166

EST:     CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG
genomic: CCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAG

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: 509

TGGCCAGCAAGGCTCATATCCAATTAAGCTGTTCTACACTTCAAACATGCCCATCATCCTTCACTCTGCGCTGATTACCAACCTCTATTTTATATCCCAGgtacacacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAGTGGAAGGAGTCTGAATACTCTGGCCATTCTATTCCTGTTGGTGGTCTTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 479

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 578

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 540

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

agtaagttatatcttctgtatgtgtaactgctaatgtattttactgctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAGTGGAAGGAGTCTGAATACTCTGGCCATTCTATTCCTGTTGGTGGTCTTG

                            tgctaat  putative branch site (score: 540)
                               taatgtattttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacacctcatttctaatgctgcagtaagttatatcttctgtatgtgtaactgctaatgtattttactgctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAGTGGAAGGAGTCTGAATACTCTGGCCATTCTATTCCTGTTGGTGGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG