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

gtaagtatttgaacatatatgatatgttgctactagtttatctctatttgatatagctgaaatagcatttgtaatatgatcttgggccgttttctttgtgcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTCTTCCTCCCACACCGTCCTCGAGGAGAAGTTTGCGAGCCACCGATTTTTC

Basic information

species	Zea mays
transcript	GRMZM2G081521_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G081521_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g01295.1 (Oryza sativa), 3'ss of exon 2

---------------------------gtaagtatttgaacatatatgatatgttgctactagtttatctctatttgatatagctgaaatagcatttgtaatatgatcttgggccgttttctttgtgcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTCTTCCTCCCACACCGTCCTCGAGGAGAAGTTTGCGAGCCACCGATTTTTC
                            ||  |   |   ||     ||| ||   ||  ||  ||   ||| | |   |||| |     |||| || || | ||   |    | |     |||||    |  ||||||||||| ||||||||||||||||||||||| ||||| ||||||||||||||||| |||||||| ||| |||||||| |||||||||| ||||||||||
gtaaagcccgtgtgaatgttctgcatgatagtttgctagtcaccatagatctggcacttttatcttgcatctctgtttcatagttttctcagcactttta-tctgcaatctaacaggcccttttgt----ttgtagGTGCAAGCACATGGAGCGGATGCAATGGTTGATGAGGACAACTGTGTGTTCTTCCTACCACACCGCCCTAGAGGAGAAATTTGCGAGCCGCCGATTTTTC

upper sequence: GRMZM2G081521_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv01s0146g00020.t01 (Vitis vinifera), 3'ss of exon 2

gtaagtatttgaacatatatgatatgttgctactagtttatctctatttgatatagctgaa-atagcatttgtaatatgatcttgggccgttttctttgtgcattg-atagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTCTTCCTCCCACACCGTCCTCGAGGAGAAGTTTGCGAGCCACCGATTTTTC
        || |    |    |  | ||  |  | ||||| ||   || |||||     |  | |  |||| |  | ||| |||     || |   |      ||| | |||||||||| |||||| | |||||||||||||| ||||| || ||||| |||||| | ||||| |||||  ||||   | |||| || || ||  | ||||
--------ttcatttgaagcaaagtatttttttttgtttaacttc-ttggatatttacaagtaaattatttatt-tttgagcttct-ttgtctcgatcccatgttgtacagGTGCAAGCACATGGATCAGATGCAATGGTTGATGAGGAAAATTGTGTTTTCTTCTTACCACATCGTCCGAGAGGTCGAATTTGTGAACCTCCCTTCTTTC

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|91872538|gb|EB402495.1|EB402495

EST:     ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTG                         GTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC
genomic: ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC

EST: gi|93016087|gb|EB641607.1|EB641607

EST:     TATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGT-                         GTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGGATAACTGTGTGTT
genomic: TATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGA-GGATAACTGTGTGTT

EST: gi|87155729|gb|DY400518.1|DY400518

EST:     ATATTGCCATTGAATGCCTAGCTACTGAGTTCAAGAGAGAAGTTTACGTG                         GTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC
genomic: ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC

EST: gi|22715158|gb|BU197608.1|BU197608

EST:     ATATTGCCATTGAATGCCTAGCTACTGAGTTCAAGAGAGAAGTTTACGTG                         GTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC
genomic: ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC

EST: gi|76011841|gb|DT939011.1|DT939011

EST:     ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTG                         GTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC
genomic: ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC

EST: gi|149110617|gb|EE294218.2|EE294218

EST:     ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTG                         GTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC
genomic: ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC

EST: gi|110530425|gb|EE034609.1|EE034609

EST:     ATATTGCCATTGAATGCCTAGCTACTGAATCCAAGAGAGAAGTTTACGTG                         GTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC
genomic: ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC

EST: gi|148935499|gb|EC879540.2|EC879540

EST:     AATTCAAGAGAGAAGTTTACGTG                         GTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC
genomic: AATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC

EST: gi|113694933|gb|DW849046.1|DW849046

EST:     ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTG                         GTGCAAGCCCA
genomic: ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCA

EST: gi|78075130|gb|DV503564.1|DV503564

EST:     ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTG                         GTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC
genomic: ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC

EST: gi|76287864|gb|DV027432.1|DV027432

EST:     ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTG                         GTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC
genomic: ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC

EST: gi|110214478|gb|EC896375.1|EC896375

EST:     ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTG                         GTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC
genomic: ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC

EST: gi|74244388|gb|DT652302.1|DT652302

EST:     ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTG                         GTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC
genomic: ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC

EST: gi|26559346|gb|CA831581.1|CA831581

EST:     ATATTGCCATTGAATGCCTAGCTACTGAGTTCAAGAGAGAAGTTTACGTG                         GTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC
genomic: ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC

EST: gi|91878642|gb|EB408599.1|EB408599

EST:     ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTG                         GTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC
genomic: ATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTC

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: 46 (upstream exon), 46 (downstream exon)
Score: 86

ACTGACAATAGATGAGAACCGAGATGGCCGTGCAGCTGCATTTGGCGATGATATTGCCATTGAATGCCTAGCTACTGAATTCAAGAGAGAAGTTTACGTGgtaagtattt ... gcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTCTTCCTCCCACACCGTCCTCGAGGAGAAGTTTGCGAGCCACCGATTTTTC

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 64

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 62

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 65

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

agctgaaatagcatttgtaatatgatcttgggccgttttctttgtgcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTCTTCCTCCCACACCGTCCTCGAGGAGAAGTTTGCGAGCCACCGATTTTTC

            atttgtaatatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatttgaacatatatgatatgttgctactagtttatctctatttgatatagctgaaatagcatttgtaatatgatcttgggccgttttctttgtgcattgatagGTGCAAGCCCATGGAGCGGATGCAATGGTTGACGAGGATAACTGTGTGTTCTTCCTCCCACACCGTCCTCGAGGAGAAGTTTGCGAGCCACCGATTTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT