ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGACCCGCTGAATGAGGAATTTGATCCTAACAGGCATTGTGCAGTTTTTCAAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaacttaaaaacaccctttttttcagcatattataggaaatccaagaatgtttagattggagttatcgggtttccgttgcattgtgtttttttc...

Basic information

species	Zea mays
transcript	GRMZM2G030312_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G030312_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os09g11250.1 (Oryza sativa), 5'ss of exon 5

TGACCCGCTGAATGAGGAATTTGATCCTAACAGGCATTGTGCAGTTTTTCAAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaacttaaaaacac-----cctttttttcagcatattataggaaatccaagaatgtt-tagattggagttatcgggtttccgttgcattgtgtttttttc
||| ||  |||||||| ||||||||||||  || ||||||||| | |||||||||||||| || || |||||  | || || || ||||||||||||||||||||  | | |  |    |      |  | |||| ||||||| | || || | ||| || || | | |  | ||||       ||  |   ||||| || |    
TGATCCTTTGAATGAGAAATTTGATCCTAGTAGACATTGTGCAATCTTTCAAATTCCTGACCCCTCGAAACCTTCAGGAACTGTAGCTTCTGTTGTAAAGgtatggaatcgtgcattttctgatatccatgtttctgcatattgtggggaacctaagcatcttgtggttaagcgttaatcatgatctatg--attgtattct----

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|148933325|gb|EC876982.2|EC876982

EST:     AAATTCCTGATCCTTCAAAACCACCCGGGACCGTTGCTTCTGTTGTAAAG                         GTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGGCGAAGTCGGCGTC
genomic: AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaac ... gtggtttcagGTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC

EST: gi|71766863|gb|DR964800.1|DR964800

EST:     AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAG                         GTGGGCTACATGTTACACGATCGCGTCCTCCGCCCT
genomic: AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaac ... gtggtttcagGTGGGCTACATGTTACACGATCGCGTCCTCCGCCCT

EST: gi|148933324|gb|EC876981.2|EC876981

EST:     AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTTTGTTGTAAAG                         GTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC
genomic: AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaac ... gtggtttcagGTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC

EST: gi|29129982|gb|CB380686.1|CB380686

EST:     AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAG                         GTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC
genomic: AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaac ... gtggtttcagGTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC

EST: gi|5124120|gb|AI745744.1|AI745744

EST:     AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAG                         GTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC
genomic: AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaac ... gtggtttcagGTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC

EST: gi|7162360|gb|AW519982.1|AW519982

EST:     AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAG                         GTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC
genomic: AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaac ... gtggtttcagGTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC

EST: gi|71770780|gb|DR968717.1|DR968717

EST:     AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGAAAAG                         -TGGGCTACATGTTACACGAT
genomic: AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaac ... gtggtttcagGTGGGCTACATGTTACACGAT

EST: gi|71439951|gb|DR821001.1|DR821001

EST:     AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAG                         GTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC
genomic: AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaac ... gtggtttcagGTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC

EST: gi|88755369|gb|DY539510.1|DY539510

EST:     AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAG                         GTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC
genomic: AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaac ... gtggtttcagGTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC

EST: gi|16925262|gb|BM078330.1|BM078330

EST:     AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAG                         GTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC
genomic: AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaac ... gtggtttcagGTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC

EST: gi|148995402|gb|EE034607.2|EE034607

EST:     AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTTTGTTGTAAAG                         GTGGGCTACATGTTACACGATCGCGTCTTCCGCCCTGCCGAAGTCGGCGTC
genomic: AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaac ... gtggtttcagGTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC

EST: gi|211470275|gb|FL336875.1|FL336875

EST:     AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAG                         GTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGC
genomic: AAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaac ... gtggtttcagGTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGC

EST: gi|78075537|gb|DV503971.1|DV503971

EST:     ATTCCTGATCCTTCAAAACCACCGGGGAACCCGT-GCTTCTGTTGTAAAG                         GTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC
genomic: ATTCCTGATCCTTCAAAACCACCGGGGA-CC-GTTGCTTCTGTTGTAAAGgtatgttaac ... gtggtttcagGTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTC

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), 48 (downstream exon)
Score: 208

TGACCCGCTGAATGAGGAATTTGATCCTAACAGGCATTGTGCAGTTTTTCAAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaac ... gtggtttcagGTGGGCTACATGTTACACGATCGCGTCCTCCGCCCTGCCGAAGTCGGCGTCACTGCCACGGAGGGAGGTGCGCATGCAACTGAAGAGGCAGAGAAGCCGG

Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 62

Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 29

Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 112

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACCCGCTGAATGAGGAATTTGATCCTAACAGGCATTGTGCAGTTTTTCAAATTCCTGATCCTTCAAAACCACCGGGGACCGTTGCTTCTGTTGTAAAGgtatgttaacttaaaaacaccctttttttcagcatattataggaaatccaagaatgtttagattggagttatcgggtttccgttgcattgtgtttttttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataggaaa