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

...taatgttcttttatcagcgttaatggaactgaatttccttgcaattcagaattctctccatttggtttacttatctcactgcagttcaatatcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCTTGTATATGACGTCACTCGCCACTCAACCTTTGAGAACGTTGAGCGTTGG

Basic information

species	Zea mays
transcript	GRMZM2G018619_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G018619_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g35814.1 (Oryza sativa), 3'ss of exon 1

taatgttcttttatcagcgttaatggaactgaatttccttgcaattcagaattctctccatttggtttacttat---ctcact-----gcagttcaatatcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCTTGTATATGACGTCACTCGCCACTCAACCTTTGAGAACGTTGAGCGTTGG
        |||| | ||   |    | ||||| ||  |||||||  |||||| ||  |  ||  |||||||| |    |||||         |    | |   |||||||||||||| || |||||||| ||||||||||| |||||||| ||||||||||| ||||| ||||| || ||||||||||||||||| |||||||| |||
--------tttttttagtagtttcagcactgatttatcttgcaaggcagaatgctgccttttcagtttacttctgccttcacttataaagcatctgttcttggtgcagATACCGTGCTATTACTAGTGCATATTACCGAGGTGCTGTTGGAGCGTTGCTTGTCTATGATGTCACCCGGCACTCAACCTTTGAGAATGTTGAGCGCTGG

upper sequence: GRMZM2G018619_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT4G18800.1 (Arabidopsis thaliana), 3'ss of exon 1

------------taatgttcttttatcagcgttaatggaactgaatttccttgcaattcagaattctctccatttggtttacttatctcactgcagttcaatatcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCTTGTATATGACGTCACTCGCCACTCAACCTTTGAGAACGTTGAGCGTTGG
            || | |  |  ||||     ||||  ||| || ||||  ||  | | ||     ||   |   |||||  || | || |  |  |||  |||   |  |||||||| |||||||||||||| || || ||||| |||||||||||| | ||||| || ||||| || || |||||||| || || ||||||||| | |||
catttcggttcttattatgttcctatcttt-ctaatttaacagagtttcaatg--actaag-----tcgttaacgggttt--ttgtttctcctcttttcgctattttt--agATACCGAGCAATCACTAGTGCTTACTATCGAGGAGCTGTTGGGGCGCTTCTTGTTTACGACGTAACCCGACACTCAACATTCGAAAACGTTGAGAGATGG

upper sequence: GRMZM2G018619_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G45750.1 (Arabidopsis thaliana), 3'ss of exon 1

taatgttcttttatcagcgttaatggaactgaatttccttgcaattca-gaattctctccattt-ggtttacttatctcactgca--gttcaat--atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCTTGTATATGACGTCACTCGCCACTCAACCTTTGAGAACGTTGAGCGTTGG
      |   |  || |  ||        | ||  | |||||  ||   |  |||      ||| |||| |||||  || |||    ||| | |   |  |   || ||||| || ||||||||||||||||||||||| |||||||| ||| | ||||| || || || || || |||||||| ||||| |||||||||  ||||
------tgcatagtctgaattcgaaactgtaaagcttcttgccttttttgtgttcctgatgtttcggttaacttaattctctgtttcgttgactttgtttcaatagGTACCGAGCCATCACTAGTGCGTATTACCGAGGAGCTGTTGGAGCGCTTCTTGTCTACGATGTAACCCGACACTCAACATTTGAAAACGTTGAGACTTGG

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|211523766|gb|FL028548.1|FL028548

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|26456776|gb|CA828359.1|CA828359

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211523764|gb|FL028546.1|FL028546

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211523763|gb|FL028545.1|FL028545

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211036214|gb|FL005942.1|FL005942

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211534479|gb|FL099191.1|FL099191

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|89758072|gb|DY687414.1|DY687414

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211036215|gb|FL005943.1|FL005943

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211523767|gb|FL028549.1|FL028549

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211036210|gb|FL005938.1|FL005938

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211523768|gb|FL028550.1|FL028550

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|85151788|gb|DW587513.1|DW587513

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211036212|gb|FL005940.1|FL005940

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|20508250|gb|BQ279941.1|BQ279941

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211523771|gb|FL028553.1|FL028553

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211523769|gb|FL028551.1|FL028551

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211036218|gb|FL005946.1|FL005946

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211036211|gb|FL005939.1|FL005939

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211523770|gb|FL028552.1|FL028552

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|211523765|gb|FL028547.1|FL028547

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|60339594|gb|DN206567.1|DN206567

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

EST: gi|60356846|gb|DN223819.1|DN223819

EST:     GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: GACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT

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: 184

AGTCCAAGTCCACCATCGGCGTCGAGTTCGCCACCCGCTCTCTCCAGGTCGACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAACGgtacgtttcg ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCTTGTATATGACGTCACTCGCCACTCAACCTTTGAGAACGTTGAGCGTTGG

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 86

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 91

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 55

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcagaattctctccatttggtttacttatctcactgcagttcaatatcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCTTGTATATGACGTCACTCGCCACTCAACCTTTGAGAACGTTGAGCGTTGG

                           atctcac  putative branch site (score: 55)
                    tttacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgttcttttatcagcgttaatggaactgaatttccttgcaattcagaattctctccatttggtttacttatctcactgcagttcaatatcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCTTGTATATGACGTCACTCGCCACTCAACCTTTGAGAACGTTGAGCGTTGG

- - - - - - - - - - - - - aactgaa
- - - - - - - - - - - - - - - - - -tccttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgcag