ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CTGCTAGAAGATTAAGGCGTGGTCCCCATACTGAGTACATTATATCTCTTGATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttcaataggattccagagttctcctgaatcttcttgtattagctctacttatgaattggttctgaaagtgatgtgttctggtgcaattaggtgg...

Basic information

species	Zea mays
transcript	GRMZM2G062154_T03
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G062154_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g48370.1 (Oryza sativa), 5'ss of exon 3

CTGCTAGAAGATTAAGGCGTGGTCCCCATACTGAGTACATTATATCTCTTGATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttcaataggattccagagtt--ctcctgaatcttcttgtattagct-ctacttatg--aattggttctga-aagtgatgtgttctggtgcaattaggtgg
|||||||||| || || |||||||||||||| ||||||||  |||| |||||||| || ||| | |||||||| |||||| |||||||||| ||||||||||||||||| | | |  | || ||||  ||| | |   |||||| ||   ||  || | ||     || || || | || |    ||   |  |  | ||      
CTGCTAGAAGGTTTAGACGTGGTCCCCATACCGAGTACATCGTATCCCTTGATGCTGATGACCTTTCACAAGGAAGCAATGCATACATGGGGAAACTGAGgtgaggttctacatggctgcatagttcactcttaatcattcttgcatattctgttattcatcctgcttagtgctaacaaattggttgcagtaatatattt------

upper sequence: GRMZM2G062154_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G35920.1 (Glycine max), 5'ss of exon 3

CTGCTAGAAGATTAAGGCGTGGTCCCCATACTGAGTACATTATATCTCTTGATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttcaataggattccagagttctcctgaa---tcttcttgtatt-agctctacttatgaattggttctgaaagtgatgtgttctggtgcaattaggtgg-
| ||||| ||||  ||| ||||| ||||||||||||| || || || |||||||| || |||||||| ||||| |||||| | ||  | ||||| || |||| | | |   |    | ||| || |      ||   ||| ||| |  | || | ||   ||  | |  || | ||  | |||   |    |||   |   |   
CAGCTAGGAGATATAGGTGTGGTACCCATACTGAGTATATAATTTCACTTGATGCTGATGACTTATCCCAAGGAAGCAATGCTTATGTTGGAAAGCTAAGgtaaagctttct----tcccatagatagaaaaaaaattctgcttatggtgaggtatagacatctagtatttgt-aagataatgccattatttgcccctttttttc

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|19272436|gb|BM888692.1|BM888692

EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA

EST: gi|7216844|gb|AW562966.1|AW562966

EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAATCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA

EST: gi|19436332|gb|BM952742.1|BM952742

EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA

EST: gi|22490595|gb|BU050518.1|BU050518

EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA

EST: gi|87152741|gb|DY397530.1|DY397530

EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA

EST: gi|19272372|gb|BM888628.1|BM888628

EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA

EST: gi|22490929|gb|BU050852.1|BU050852

EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA

EST: gi|22491102|gb|BU051025.1|BU051025

EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA

EST: gi|19058652|gb|BM737319.1|BM737319

EST:     GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAG                         ATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA
genomic: GATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATA

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: 185

CTGCTAGAAGATTAAGGCGTGGTCCCCATACTGAGTACATTATATCTCTTGATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttca ... ccctgtttagATCTGATTTCTGGGGGACAAACTTCAAAATATATGATAGCAAGCCACCATATGACGGCGCTAAAGCATCAAGTAGTCGATCTAGTCGTCGTTTCGGAAGC

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 122

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 148

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCTAGAAGATTAAGGCGTGGTCCCCATACTGAGTACATTATATCTCTTGATGCAGAGGACTTATCACAAGGGAGCAATTCATACATGGGAAAACTGAGgtgaggttcaataggattccagagttctcctgaatcttcttgtattagctctacttatgaattggttctgaaagtgatgtgttctggtgcaattaggtgg

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA