ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGATCACCGACCGCGATCTGGTGTCTGGAAAGGCACTAGTGGTGGGGAAGCTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttctagatccactcctcaacaatttattgcagtcatgtctatgtgctactctttaaattatgaggcgagtctgtttaagggactgctggcagatc...

Basic information

species	Zea mays
transcript	GRMZM2G035928_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G035928_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT1G02170.1 (Arabidopsis thaliana), 5'ss of exon 3

AGATCACCGACCGCGATCTGGTGTCTGGAAAGGCACTAGTGGTGGGGAAGCTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttctagatccactcctcaacaatttattgcagtcatgtctatgtgctactctttaaattatgaggcgagtctgtttaagggactgctggcagatc
 ||||| || ||  | || ||| | |||||||| |||  |||||| ||||| |||||  ||||||| ||||||||||||||||| || || || || || ||||||   ||| | ||||       |  | |||| ||  |   |   | || ||||    ||||  |  |                             
GGATCATCGGCCTAGGTCAGGTTTGTGGAAAGGAACTGCTGGTGGAGAAGCCATTTCAATTAGTGGATGTGATGATGATCAGACTTCGGCCGACACATCAgtaagt---agaacgactctaatcatacgtcttgctgttgtagttggttcctcctctcatgattaaaacacatacacag---------------------

upper sequence: GRMZM2G035928_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv15s0021g00990.t01 (Vitis vinifera), 5'ss of exon 5

AGATCACCGACCGCGATCTGGTGTCTGGAAAGGCACTAGTGGTGGGGAAGCTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttctagatccactcctcaacaat--ttattgca-gtcatgtct----atgtgctact---ctttaaattatgaggc-gagtctgttta-agggactgctggcagatc--
 || || || || | ||| ||||| |||||||| || | |||||| ||||  ||||||||||||||||||||||||||||| || ||||| ||||| ||||||||||   ||   |||  | |   ||  |  ||  |  || | | |    |  || | |    | | | |  |  | ||  | | ||| || |  || | ||    || |  
GGACCATCGCCCTCAATCAGGTGTATGGAAAGGAACAAATGGTGGAGAAGTCATTTCCTTTAGTGGTTGTGATGATGATCAAACATCTGCTGATACATCTgtaagtttcggaatgactgattagacatagtccttatatatcttattttcccaattgtttcaagacctcagaccaaaaagctaaatatgtgtatactgatttctttgggaacag

upper sequence: GRMZM2G035928_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv16s0013g00220.t01 (Vitis vinifera), 5'ss of exon 3

AGATCACCGACCGCGATCTGGTGTCTGGAAAGGCACTAGTGGTGGGGAAGCTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaa---gttctagatcc-actcctcaacaatttattgcagtcatgtctatgtgctactctttaaattatgaggcgagtctg---tttaagggactgctggcagatc-------------
 || || || || | ||| ||  | |||||||| || ||||||||||| |  ||||||||||| || ||||||||| |||| |||||||| ||||| || ||||    || |  || | | |  ||  |  || |||  | |   || |      || |  | |  | |  | |  |  |     || |||  | ||||   ||                
GGACCATCGCCCCCCATCAGGCATATGGAAAGGAACAAGTGGTGGGGAGGTCATTTCCTTTAGCGGCTGTGATGATAATCAAACCTCTGCTGATACGTCGgtaatgcattatgcattctatttttcttcttttgatttaactagagtatcaagaatatttctcagctgaccatggaaaacaaaccttcaagctaatgcttttagccttttatgtgggcag

upper sequence: GRMZM2G035928_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv16s0013g00210.t01 (Vitis vinifera), 5'ss of exon 3

AGATCACCGACCGCGATCTGGTGTCTGGAAAGGCACTAGTGGTGGGGAAGCTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagt--tctagatccac---tcctcaac--aatttattgcagt----catgtctat--gtgctact-ctttaaattatgaggcgagtctg---tttaagggactgctggcagatc-----
||| || || || ||||| ||||| |||||||| || ||||||||||| |  ||||| |||||||||||||||||| |||| | |||    |||||    |||||   | || || |     | || | |  ||||| ||  | |    | || ||||    | || | || ||| | |  | |  |  |     || |||  | ||||    |||      
AGACCATCGCCCTCGATCAGGTGTATGGAAAGGGACAAGTGGTGGGGAGGTCATTTCTTTTAGTGGTTGTGATGATCATCAAATCTCCATTGATACACGAgtaagcaatataaattctaatattcttatcttaatttcttttaattcaacttgactatcaaagatatttctctaactcacaatgaaaaccaaactttaaagctaatgctttgtgatatatag

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|91053235|gb|EB163653.1|EB163653

EST:     CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCT                         GCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA
genomic: CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttcta ... ttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA

EST: gi|91875164|gb|EB405121.1|EB405121

EST:     CTATTTCCTTTAGTGGTTGGGATGATGATCAGACCTCTGCAGATACCTCT                         GCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTTTGCTTCATCCAA
genomic: CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttcta ... ttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA

EST: gi|71759837|gb|DR957774.1|DR957774

EST:     CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCT                         GCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGTTTCATCCAA
genomic: CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttcta ... ttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA

EST: gi|93016581|gb|EB642101.1|EB642101

EST:     CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCT                         GCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA
genomic: CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttcta ... ttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA

EST: gi|148976593|gb|EE025939.2|EE025939

EST:     CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCT                         GCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA
genomic: CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttcta ... ttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA

EST: gi|50337462|gb|CO532588.1|CO532588

EST:     CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCT                         GCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA
genomic: CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttcta ... ttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA

EST: gi|91055205|gb|EB165623.1|EB165623

EST:     CTATTTCCTTTAGTGGTTGTGGTGATGATCAGACCTCTGCAGATACCTCT                         GCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTTTGTTTCATCCAA
genomic: CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttcta ... ttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA

EST: gi|78079402|gb|DV507814.1|DV507814

EST:     CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCT                         GCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA
genomic: CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttcta ... ttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA

EST: gi|76911371|gb|DV164249.1|DV164249

EST:     CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCCGCAGATACCTCT                         GCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA
genomic: CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttcta ... ttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA

EST: gi|193502060|gb|AM937871.1|AM937871

EST:     CTATTTCCCTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCT                         GTTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA
genomic: CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttcta ... ttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA

EST: gi|89246802|gb|DY618589.1|DY618589

EST:     CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCT                         GCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA
genomic: CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttcta ... ttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA

EST: gi|93016582|gb|EB642102.1|EB642102

EST:     CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCT                         GCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA
genomic: CTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttcta ... ttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA

EST: gi|91049155|gb|EB159573.1|EB159573

EST:     TTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCT                         GCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA
genomic: TTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttcta ... ttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAA

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), 44 (downstream exon)
Score: 43

AGATCACCGACCGCGATCTGGTGTCTGGAAAGGCACTAGTGGTGGGGAAGCTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttcta ... ttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAAGCTATTGAACGTGGACAGGGCACCACCTACGGTAGTATCCTGAACTCTA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

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

Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 89

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATCACCGACCGCGATCTGGTGTCTGGAAAGGCACTAGTGGTGGGGAAGCTATTTCCTTTAGTGGTTGTGATGATGATCAGACCTCTGCAGATACCTCTgtaagttctagatccactcctcaacaatttattgcagtcatgtctatgtgctactctttaaattatgaggcgagtctgtttaagggactgctggcagatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT