ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcattatcttagtacttaataatatgtgtgagcaatttgttatagccgagttatttgataaagtttcatatgtgctcaagcccattctcctcaaat...

Basic information

species	Zea mays
transcript	GRMZM2G083262_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G083262_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g18510.1 (Oryza sativa), 5'ss of exon 3

TATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcattatctt-agt---acttaataatatgtgtgagcaatttgttatagccgagttatttgataaagtttcatatgtgctcaagcccattctcctcaaat
 |||| ||| ||||||||||| || |||||||| ||||| |||||||||||||||||||| ||||||||||||||  |||||||||| || ||||||||||| ||   | |||| ||      ||  | ||    |||     |   || |    ||   ||  |||  |   | ||      | |  ||     |   ||   
CATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctttcttcagcttattttgttgattatcgtggatcttgcattgtgcttgaccgataagatgga--ctaattcacatttagaccatagttgtacat--

upper sequence: GRMZM2G083262_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G35600.1 (Glycine max), 5'ss of exon 5

TATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcattatcttagta-----cttaataatatgtgtgagc----aatttgttatagccgagttatttgataaagtttcatatgtgctcaagcccattctcctcaaat
 ||| | || ||||||||||| || |||||| |||| || || || ||||| || |||||||| |||||||||||| | ||||| ||||| || ||||||||| |    || ||   |     ||| || || | | | |       || | | |     |       || |  | | |      || |   |  ||||          
AATGCATAAGGCTGAAGCTGCAGGAAATGATGACTGCCCCGTCAAAATTAAACTTGTTGCTCCCCCACTTTATGTTCTTACCACCCAGACACTGGACAAGgttagtgcaattttcacataaatcttgattatgtatataatttttggatgtatgaattttgcccctactgttgtattgtagataatgtttgggggcattt---------

upper sequence: GRMZM2G083262_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G02820.1 (Glycine max), 5'ss of exon 5

TATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcattatcttagta-----cttaataatatgtgtgagcaatttgt-tatagccgagttatt--tgataaagtttcatatgtgctcaagcccattctcctcaaat
 |||   || |||||||||| ||| |||||| |||| ||||| || ||||| || |||||||| |||||||||||| | ||||| ||||| || ||||||||| |    || |||  |     ||| || ||   | | |    |   | |||      |  | |  || |  | | |    | || |  ||  ||||          
AATGCGTAAGGCTGAAGCTGTGGGAAATGATGACTGCCCTGTCAAAATTAAACTTGTTGCTCCCCCACTTTATGTTCTTACCACCCAGACACTGGACAAGgttagtgcaattttaacataaatcttgattatgcatataatttttggatgtatgaatttgccactgctgctgcattgtagattatgtttgagggcatttg--------

upper sequence: GRMZM2G083262_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv13s0067g01710.t01 (Vitis vinifera), 5'ss of exon 5

TATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgt--tggcattatcttagtacttaataatatgtgtgagcaatttgttatagccgagttatttgataaagtttcatatgtgctcaagcccattctcc---tcaaat--
 |||  |||||| ||||| ||||||||| |  | ||||| ||||| ||||| || ||||||||||| ||||||||| | || || ||||| |||||||||||  || ||   | | || |   |||  |     ||   ||||  |||| |||    | |||  ||  |   || |  || |    ||  ||       |  |||  
AATGCGGAAAGCAGAAGCGGCGGGCAATAAGGATTGTCCAGTGAAAATTAAACTGGTTGCTCCTCCGCTTTATGTTCTTACTACTCAGACGCTTGACAAGgtaatgacacagtgt-agcaaacaatt-tccccctggataatt--ttattgcctg--tgtttagtacggag-caaacttgtttcctcctttttggtgggttgaatgg

upper sequence: GRMZM2G083262_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv06s0004g07100.t01 (Vitis vinifera), 5'ss of exon 5

TATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcattatcttagtacttaataatatgtgtgagcaatttgttatagccgagttatttgataaagtttcatatgtgctcaagcccattctcctcaaat-------
||||   |||||||||||||| |||||| |  |||| |||||||| || ||  | ||||||||||| || |||||| | ||||| || || |||||||||||  ||      ||   | ||||   | |   ||  ||  ||||| |  || | |   |||||  ||     | |    | | | |  |  |     | |       
TATGCGTAAAGCTGAAGCTGCCGGCAATAAAGACTGCCCTGTGAAAATAAAATTGGTTGCTCCTCCCCTCTATGTTCTAACCACTCAAACTCTTGACAAGgtaagc------ttgagatttaactgtgtaactggtcatcttgtt-tcccctactatgttgatgtaggcaagttttcttttatgactttgttttctcattattcact

upper sequence: GRMZM2G083262_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S55_319V6.1 (Physcomitrella patens), 5'ss of exon 6

TATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcattatcttagtacttaataatatgtgtgagc--aatttgttatagccgagttattt--gataaagtttcatatgtgctcaagcccattctcctcaaat--------------------------------------------------------------------
 ||||  || || || ||||| || | |||  | |||||||||||||||||| |||| || || |||||||||||  | ||||||||||| |||||||||||  |    ||||   || ||  |   || |  ||    ||       |     |   ||     | | |  ||||||| |     |||  |        |||                                                                     
AATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaatctacatattttgtgggatttaagattttaaaccaggttgataaatacatcccaaacagatgttcatatattggtcagcttacatcgaataaacatgaaatgctaccgttttagtttttactattttcaaagctcgtattcaacttgtgcattgcttgtcag

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|4966988|gb|AI691994.1|AI691994

EST:     AGCTAGTTGCTCCTCCNCTTTATGTTTTGACCNCACAGACCCTTGNCAAG                         GATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|61117519|gb|DN558480.1|DN558480

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|37390451|gb|CF632455.1|CF632455

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|60400978|gb|DN233785.1|DN233785

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|60337847|gb|DN204820.1|DN204820

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|60351270|gb|DN218243.1|DN218243

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|74235505|gb|DT643419.1|DT643419

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|166571705|gb|EG281233.1|EG281233

EST:     CTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: CTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|24763866|gb|CA399037.1|CA399037

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|37381588|gb|CF627690.1|CF627690

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|60353715|gb|DN220688.1|DN220688

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|29577089|gb|CB617201.1|CB617201

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|60352316|gb|DN219289.1|DN219289

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|60400924|gb|DN233731.1|DN233731

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|60351973|gb|DN218946.1|DN218946

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|28982561|gb|BQ538174.2|BQ538174

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|4804073|gb|AI665939.1|AI665939

EST:     AGCTAGTTGCTCCTCC-CTTTATGTTTTGACC-CCCAGACCCTTGACAAG                         GATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|13149573|gb|BG319895.1|BG319895

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|60354041|gb|DN221014.1|DN221014

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

EST: gi|78023586|gb|DV491973.1|DV491973

EST:     AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAG                         GATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG
genomic: AGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAG

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: 317

TATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcatta ... ctttgaacagGATCAAGGCATTTCAGTTCTCACTACTGCAGTCAAGGCTTGTACAGCAGAGATTGAAAAGTACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 220

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 274

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcattatcttagtacttaataatatgtgtgagcaatttgttatagccgagttatttgataaagtttcatatgtgctcaagcccattctcctcaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC