ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ACAAGAAATAGTAAATAATACTAAGTTGAGTGAGGGATATCTTACTCTTGCTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgtgatgtatattttactgcttatcatatttttaatagcatgattaaatcctctataataattatgatcatgttttacaatatgtag

Basic information

species	Zea mays
transcript	GRMZM2G314233_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G314233_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 5'ss of exon 12

ACAAGAAATAGTAAATAATACTAAGTTGAGTGAGGGATATCTTACTCTTGCTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgtgatgtatattttactgcttatcatatttttaatagcatgattaaatcctctataataatta-tgatcatgttttacaatatgtag
 |||||||| || ||||||| |||| |||||||||| || || || |||||||| ||||| || || |||||  | ||||| |||||||||||||| ||||| || |||||||||||    ||    ||| | |  |  || ||   || |  |||||||||| |  |  | ||| ||||| |  ||
GCAAGAAATCGTTAATAATAGTAAGCTGAGTGAGGGGTACCTCACCCTTGCTCGAGATATCGAAGTGATGGAAGCAAAATCTCCAGAGGATATATATAAGgtcatctatattttactatcaat---gtttattaaggt-tgcttttttcattcataataattaatatttgtatttaacaatctacag

upper sequence: GRMZM2G314233_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 12

ACAAGAAATAGTAAATAATACTAAGTTGAGTGAGGGATATCTTACTCTTGCTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgtgatgtatattttactgcttatcatatttttaatagcatgattaaatcctctataataattatgatcatgttt---tacaatatgtag-----------------
 || |||||  |||| ||| ||||||| ||||| |||||||| || |||||||| |||||||| ||||||||||| || ||||| |||||||||||||||||| ||   |||||  |  | ||  || ||||  ||  ||   | ||  || ||  | |  ||   || ||||     ||| ||| ||                  
GCAGGAAATCATAAACAATTCTAAGTTAAGTGAAGGATATCTCACCCTTGCTCGTGATATTGAAGTCATGGAGCCCAAGTCCCCTGAGGATATATACAAGgtg-tg---attttgattataattttacttttgctataata--tgaactctgtaccagatataacttcctgttcatgcacagtatttaaatctaatgccctgaaat

upper sequence: GRMZM2G314233_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA12G13410.1 (Glycine max), 5'ss of exon 12

ACAAGAAATAGTAAATAATACTAAGTTGAGTGAGGGATATCTTACTCTTGCTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgtgatgtat--------attttactgct--tatcatatttttaatagcatgattaaatcctctataataattatg---atcatgttttacaatatgtag-
 || |||||  |||| ||| ||||||| ||||| |||||||| || |||||||| |||||||||||||||||||| || ||||| ||||||||||||||||||   | |        ||||||||  |  ||| || |  |   ||  |    ||| | |    | ||    | |   |||||| | |    | ||||  
GCAGGAAATCATAAACAATTCTAAGTTAAGTGAAGGATATCTCACCCTTGCTCGTGATATTGAGGTCATGGAGCCCAAGTCCCCTGAGGATATATACAAGgtgtgatcttgattgtaattttacttttgttataatgtactctttactagatataacttcctgttcatgtacaagtgaatcatgatcttttttttgtata

upper sequence: GRMZM2G314233_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 5'ss of exon 10

ACAAGAAATAGTAAATAATACTAAGTTGAGTGAGGGATATCTTACTCTTGCTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgtgatgtatattttactgcttatcatatttttaatagcatgattaaatcctctataataattatgatcatgttttacaa-tatgtag------------
||| || || || || ||  ||||||||||||| |||||||| || |||||| | |||||||||||||||||| | ||  | || || || || |||||||| || |   ||| | ||  ||| || | | | |  |  | |||   |        ||  |||||    ||  |   |  | |  |             
ACAGGATATTGTTAACAACTCTAAGTTGAGTGAAGGATATCTGACGCTTGCTAGGGATATTGAGGTCATGGAGGCCAAGACGCCTGAAGACATCTACAAGgt-atatcagtttaattgaatattatgtctgttactggtttatttggttacaggatatgtttatggaagtgcctcttacctgtccactgaaatttgcag

upper sequence: GRMZM2G314233_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT2G20580.1 (Arabidopsis thaliana), 5'ss of exon 10

ACAAGAAATAGTAAATAATACTAAGTTGAGTGAGGGATATCTTACTCTTGCTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgtga-------tgtatatttta---ctgcttatcatatttttaatagcatgattaaatcctctataataattatgat-catgttttacaatatgtag
||| || || || || || |||||||| ||||| |||||||| || |||||  | |||||||||||||||||| | ||| | || || || || |||||||| |       |  || | |||    ||||  |||| | |||| |  ||  ||||  |   |   | |  ||    | |   ||||  | | | |||
ACAGGATATTGTTAACAACACTAAGTTAAGTGAAGGATATCTGACCCTTGCAAGGGATATTGAGGTCATGGAGGCCAAAACGCCTGAAGACATCTACAAGgtaaatcagttttaatgtgttaggcttgctactcatttatttagttaca-aattatgtttccctcagtctttgacctgccctttttgaattttatag

upper sequence: GRMZM2G314233_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 12

ACAAGAAATAGTAAATAATACTAAGTTGAGTGAGGGATATCTTACTCTTGCTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgt---gatgtata------ttttactgctt--atcatatttttaata--gcatgattaaatcctctataataattatgatcatgttttacaatatgtag-
 || || ||  | ||||| | |||  | ||||| || ||||||||||||||||| ||||| ||||| |||||||| ||||| || || ||||| || |||||   ||  | ||       |||| | ||   |   ||  |||   |    ||| ||   |  |   |    ||  ||||    || |        ||  
GCAGGACATCATTAATAACAGTAAACTAAGTGAAGGTTATCTTACTCTTGCTCGTGATATAGAGGTGATGGAGCCCAAATCTCCTGAAGATATCTATAAGgtttggacttttagaatctctttagtactggaactgtaactttgtcactatatggttgggttttagctttggatcttgatggctttattttgctaataat

upper sequence: GRMZM2G314233_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S414_22V6.1 (Physcomitrella patens), 5'ss of exon 12

ACAAGAAATAGTAAATAATACTAAGTTGAGTGAGGGATATCTTACTCTTGCTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgtg-atgtatattttactgcttatcatattt---ttaat--agcatgattaaatc---ctctataa----taattatgatcatgtttta--caatatgtag
 |||||  || | |  || |  || ||||| ||||| ||||||||||| ||||||||| |||| |||||||| |||||| |||| || ||  |||| |||||      | ||  |  || | || || |||   ||| |  |  ||| || | |    ||   |||    | | |||    ||   |||  | | |  || 
TCAAGAGCTAATCAGCAACAGCAAATTGAGCGAGGGCTATCTTACTCTAGCTCGCGATCTTGACGTCATGGAACCTAAAACCCCGGATGACCTATATAAGgttcgcagacatcctg-tgataattatgtttaccttagtttattatgcttgagtttgactacctaacgtttgagtatagctataaattagtctaaacataa

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|19057964|gb|BM736631.1|BM736631

EST:     CTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATNCAAG                         GTCCATTTGATTGATGGCCGTGGTGCCAGCTCCAGTCTTGATTCCGCAAGA
genomic: CTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgtgatgtata ... caatatgtagGTCCATTTGATTGATGGCCGTGGTGCCAGCTCCAGTCTTGATTCCGCAAGA

EST: gi|32845420|gb|CD985101.1|CD985101

EST:     CTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAG                         GTCCATTTGATTGATGGCCGTGGTGCCAGCTCCAGTCTTGATTCCGCAAGA
genomic: CTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgtgatgtata ... caatatgtagGTCCATTTGATTGATGGCCGTGGTGCCAGCTCCAGTCTTGATTCCGCAAGA

EST: gi|32844567|gb|CD984248.1|CD984248

EST:     CTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAG                         GTCCATTTGATTGATGGCCGTGGTGCCAGCTCCAGTCTTGATTCCGCAAGA
genomic: CTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgtgatgtata ... caatatgtagGTCCATTTGATTGATGGCCGTGGTGCCAGCTCCAGTCTTGATTCCGCAAGA

EST: gi|87151923|gb|DY396712.1|DY396712

EST:     CTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAG                         GTCCATTTGATTGATGGCCGTGGTGCCAGCTCCAGTCTTGATTCCGCAAGA
genomic: CTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgtgatgtata ... caatatgtagGTCCATTTGATTGATGGCCGTGGTGCCAGCTCCAGTCTTGATTCCGCAAGA

EST: gi|20300205|gb|BQ163148.1|BQ163148

EST:     CTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAG                         GTCCATTTGATTGATGGCCGTGGTGCCAGCTCCAGTCTTGATTCCGCAAGA
genomic: CTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgtgatgtata ... caatatgtagGTCCATTTGATTGATGGCCGTGGTGCCAGCTCCAGTCTTGATTCCGCAAGA

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: 226

ACAAGAAATAGTAAATAATACTAAGTTGAGTGAGGGATATCTTACTCTTGCTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgtgatgtata ... caatatgtagGTCCATTTGATTGATGGCCGTGGTGCCAGCTCCAGTCTTGATTCCGCAAGACAGAATTTAGCTGCAACATTTGTAAATGCATTTGTGAATGCTGGGTTTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 177

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAAGAAATAGTAAATAATACTAAGTTGAGTGAGGGATATCTTACTCTTGCTCGCGATATTGAGGTCATGGAGCCTAAATCCCCAGAGGATATATACAAGgtgatgtatattttactgcttatcatatttttaatagcatgattaaatcctctataataattatgatcatgttttacaatatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT