ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GGAGCAGATAAACATAACCCGTAAAAAATACAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctcttactcctgttggaagtttggctttgtaaaattttctatccgcatgtgtttgacacttgccttggaatag

Basic information

species	Zea mays
transcript	GRMZM2G109039_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G109039_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 3

GGAGCAGATAAACATAACCCGTAAAAAATACAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctcttactcctgttggaagtttggctttgtaaaattttctatccgcatgtgtttgacacttg---ccttggaatag
|||| || ||   || || ||| | |||||||||||| |||||||||| |||||||| |||||||||||  | ||||| |||||||||| |||    |||||  |        |||| ||| ||| |   || |||| || | ||| |  |  |||| |||||| |||   | |  | | ||
GGAGAAGCTAGCGATCACACGTGATAAATACAGACAGACCAGATTAGATCAGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtgcg--------tccttttgaaagctca-ctgtgtagaactgtctgt--gtttgtgcttgacagttgacacttgtgtacag

upper sequence: GRMZM2G109039_T03 (Zea mays), 5'ss of exon 3
lower sequence: AT3G13340.2 (Arabidopsis thaliana), 5'ss of exon 3

GGAGCAGA-TAAACATAACCCGTAAAAAATACAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctcttactcctgttggaagtttggctttgtaaaattttctatccgcatg--tgtttgacacttgccttggaatag------
 |  |||| | || ||  |  |  | |||||||||||  | |||||||||||||| || |||||||| ||||| ||||| |||||||||  | |    |||||  |  |  ||  |    ||    | |   | | | |   ||    |  ||         | | || |   || | || |      
-GGACAGACTTAATATTTCTAGAGAGAAATACAGACAAACTAGATTAGAACAGTATAAGAATTATGAAAATGTCCCTAATTCTGGAGAATCATCAGAAAAGgtaagggttatatcctc--tgatcctctatttgtattagtgttcaggttagctcagtcacctaatacatcattttgtatggattcag

upper sequence: GRMZM2G109039_T03 (Zea mays), 5'ss of exon 3
lower sequence: AT1G55680.1 (Arabidopsis thaliana), 5'ss of exon 3

GGAGCAGATAAACATAACCCGTAAAAAATACAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctcttactcctgttggaagtttggctttgtaaaattttctatccgcatgtgtttgacacttgccttggaatag---------------------------
|||   | | |  || ||  |  | | |||||||||  | ||| |||||||||| ||||||||||| ||||| ||||||||||| |||    |   ||| ||  | ||   | ||    ||     | || ||| |    |||  | |     | |   | | | | |  ||  | |                             
GGACAGGCTTAGTATTACGAGAGAGACATACAGACAAACTAGACTAGAACAGTATAAAAATTATGAAAATGTCCCTAACTCTGGGGAATCTTCAGGGAAAgtaagtcttccattctctatgtctcgtaggttttct---ttttcttctatatgtttcactaatattgggtttcaactgatacttatcatttgcttaatgaattcag

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|211166255|gb|FL395975.1|FL395975

EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT

EST: gi|211150113|gb|FL386529.1|FL386529

EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT

EST: gi|20301188|gb|BQ164131.1|BQ164131

EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT

EST: gi|20301181|gb|BQ164124.1|BQ164124

EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT

EST: gi|20300911|gb|BQ163854.1|BQ163854

EST:     AAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCANCAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT

EST: gi|20300918|gb|BQ163861.1|BQ163861

EST:     AAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT

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: 471

GGAGCAGATAAACATAACCCGTAAAAAATACAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 478

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 596

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 484

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCAGATAAACATAACCCGTAAAAAATACAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctcttactcctgttggaagtttggctttgtaaaattttctatccgcatgtgtttgacacttgccttggaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC