ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ACCGGGTGCTTGGAGTTTCAGGTCTCCGGGTGGTTGACGGCTCAATATTTTCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacctcacacagttgaaacttccttgttttgctacaaaagtttaaactctaagtgtagagactgaatagctttttgtcgtactttttgttcag

Basic information

species	Zea mays
transcript	GRMZM2G081841_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G081841_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os09g19930.1 (Oryza sativa), 5'ss of exon 5

ACCGGGTGCTTGGAGTTTCAGGTCTCCGGGTGGTTGACGGCTCAATATTTTCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacctca-cacagttgaaacttccttg---ttttgctacaaaagtttaaactctaagtg--tagagactgaatagctttttgtcgtactttttgttcag
|||| |||||||||||||||||  |||| || || || ||||||| |||||||| ||| |||||||| ||||||||||| || || |||||||||||||||||||  | | ||  | |     |||||| ||    |||  |||   |  ||  |||| |||     || ||||| ||| ||||    || || ||  |  ||||
ACCGTGTGCTTGGAGTTTCAGGCGTCCGTGTAGTCGATGGCTCAACATTTTCTAGATCACCAGGGACGAACCCTCAAGCCACGGTCATGATGATGGGCAGgtacataaacacagtaaaaaattaacttctttagtctttacctaatgatattctaactttaaactcttaaagactaaattgcttccc-tcatatttcatactcag

upper sequence: GRMZM2G081841_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA15G02790.1 (Glycine max), 5'ss of exon 5

ACCGGGTGCTTGGAGTTTCAGGTCTCCGGGTGGTTGACGGCTCAATATTTTCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtac----------agtacctcacacagttgaaacttccttgttttgctacaaaagtttaaactctaagtgtagagactgaatagctttttgtcgtactttttgttcag
|   ||| ||||| |||    | ||||| |||||||| ||||||| ||||||| | || ||||| ||||||||||||||||| || |||||||||||||||||           || || | |||| |   |||| || |||  ||             |    |||  | ||||   |     ||    |    ||||  |       
ATAAGGTTCTTGGTGTTGATAGACTCCGTGTGGTTGATGGCTCAACATTTTCTGAGTCACCAGGAACCAACCCTCAAGCTACTGTGATGATGATGGGCAGgtatgtacatatatagaacataacactgagtaaacatctttggattaactttgttaccaacttactatatatagaagttagggcgccaaat----tactaataa-----

upper sequence: GRMZM2G081841_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G42630.1 (Glycine max), 5'ss of exon 5

ACCGGGTGCTTGGAGTTTCAGGTCTCCGGGTGGTTGACGGCTCAATATTTTCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacctcacacagttgaaacttccttgttttgctacaaa---agtttaaactctaagtgtagagactgaatagctttttgtcgtactttttgttcag
|   ||| ||||| |||    | || || |||||||| ||||||| ||||||| | |||||||| |||||||||||||| || || |||||||||||||||||  |||| |     |  | ||   |   |      ||    |   | |||    | | | | |    ||  |  |  | ||  |  |   |||||||   
ATAAGGTTCTTGGTGTTGATAGACTTCGTGTGGTTGATGGCTCAACATTTTCTGAGTCGCCAGGAACCAACCCTCAAGCCACTGTGATGATGATGGGCAGgtat-gtacatagagaacataaacactgagtaaacatctttggattgacttttttttattattattattacc-agcaaatgttaattatgagttttgttagt

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|45846849|gb|CN070792.1|CN070792

EST:     TCTAAATCGCCAGGGACCAACCCTCGAGCTACAGTTATGATGATGAGCAG                         ATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGG-ACAGAGCAGCTGGAG
genomic: TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGAC-GAGCAGCTGGAG

EST: gi|166476685|gb|EG040224.1|EG040224

EST:     AGTTATGATGATGGGCAG                         ATATATGGGAGTAGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAG
genomic: AGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATATGGGAGT-GAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAG

EST: gi|14364854|gb|BG946665.1|BG946665

EST:     TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAG                         ATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT
genomic: TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT

EST: gi|78108496|gb|DV526914.1|DV526914

EST:     TTTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAG                         ATATATGGGAGTGAAGATCTTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT
genomic: TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT

EST: gi|14244380|gb|BG842419.2|BG842419

EST:     TTTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAG                         ATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT
genomic: TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT

EST: gi|78116130|gb|DV534518.1|DV534518

EST:     TTTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAG                         ATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT
genomic: TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT

EST: gi|101383076|gb|EB813590.1|EB813590

EST:     TTTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAG                         ATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT
genomic: TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT

EST: gi|78073622|gb|DV502056.1|DV502056

EST:     TTTAAATCGCCAGGGGCCAACCCTCAAGCTACAGTTATGATGATGGGCAG                         ATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGG
genomic: TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT

EST: gi|71759344|gb|DR957281.1|DR957281

EST:     TTTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAG                         ATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT
genomic: TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT

EST: gi|148929608|gb|EC876001.2|EC876001

EST:     TTTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAG                         ATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT
genomic: TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT

EST: gi|50323477|gb|CO518603.1|CO518603

EST:     TTTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAG                         ATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT
genomic: TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT

EST: gi|37425550|gb|CF650521.1|CF650521

EST:     TTTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAG                         ATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT
genomic: TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT

EST: gi|161590897|gb|EY960684.1|EY960684

EST:     TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAG                         ATATAGTGGGAGTGAAGATCC
genomic: TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATA-TGGGAGTGAAGATCC

EST: gi|110481180|gb|EE010977.1|EE010977

EST:     TTTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAG                         ATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT
genomic: TCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGT

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: 316

ACCGGGTGCTTGGAGTTTCAGGTCTCCGGGTGGTTGACGGCTCAATATTTTCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacc ... ttttgttcagATATATGGGAGTGAAGATCCTAAGGGAAAGGCTGGGACGAGCAGCTGGAGTGTAGTCGATTCCTGGACATTAGCTTTTTATTATGTGTGGCCTAGGAAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

Block sizes: 44 (upstream exon), 29 (downstream exon)
Score: 6

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCGGGTGCTTGGAGTTTCAGGTCTCCGGGTGGTTGACGGCTCAATATTTTCTAAATCGCCAGGGACCAACCCTCAAGCTACAGTTATGATGATGGGCAGgtacagtacctcacacagttgaaacttccttgttttgctacaaaagtttaaactctaagtgtagagactgaatagctttttgtcgtactttttgttcag

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