ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TCTAGGGAGGTTCAACACGAAGGCGTGCGTGTCCAACGTCACCGTACGAGATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcccgtacgtcagaataatgcagtagcaggcagcagcagcaggcctaataattactaataaacctttgcag

Basic information

species	Zea mays
transcript	GRMZM2G002034_T02
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G002034_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g50260.1 (Oryza sativa), 5'ss of exon 4

TCTAGGGAGGTTCAACACGAAGGCGTGCGTGTCCAACGTCACCGTACGAGATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgcc---gcccgtacgtca---gaataatgcagtagcaggcagca-gca-gcaggcctaataattactaataaacctttgcag
|||||| |||| |||||| || || || || ||||| ||||||||| |||||||||| |||||||  |||| ||| |||||||||||||| || ||||||||| ||     |  |||  | |   || || | ||  |     || ||   |  |||  |||| ||  ||| | |  ||| |||||
TCTAGGAAGGTACAACACAAAAGCATGTGTATCCAATGTCACCGTAAGAGATGTCAACATGTTCAAAACAATGACTGGTGTCAGAATCAAAACTTGGCAGgtaagcataatctggtagatgatgtgactagtccaacaatgaccaccatatacacagagctaaaaaacactgacattcctatgcag

upper sequence: GRMZM2G002034_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv14s0066g01060.t01 (Vitis vinifera), 5'ss of exon 6

TCTAGGGAGGTTCAACACGAAGGCGTGCGTGTCCAACGTCACCGTACGAGATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacg------ccgcccgtacgtcagaataatgcagtag-caggcagcagcagcaggcctaataattactaataaac--ctttgcag-----------------------------------------------------------------------------------
||||||||||   ||||| || || |||||    || ||||| || |||||  |||  |||      |||| ||| |||||||||||||||||||||||||||        |  ||  | |  ||      | |  ||  ||  | | ||    | |      ||        || |  || || |                                                                                    
TCTAGGGAGGGATAACACCAAAGCCTGCGTAAAAAATGTCACGGTTCGAGACATCACAATGCAGGATACAATGACTGGTGTCAGAATCAAGACATGGCAGgtaaaagcatcctaccactcctccaagtcccttctctaatcatcctgaagggaaaaggggggaaacggaaggaaagcagctctgaaaaacacaataatgctacaatttattcagacgcctctgatatatgatctccaaccatctcatagttttatcatttggcactgcag

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|6538974|gb|AW225113.1|AW225113

EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG

EST: gi|71760132|gb|DR958069.1|DR958069

EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG

EST: gi|89763933|gb|DY690920.1|DY690920

EST:     GACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: GACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG

EST: gi|94475995|gb|EB704953.1|EB704953

EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG

EST: gi|37384129|gb|CF629114.1|CF629114

EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG

EST: gi|74238758|gb|DT646672.1|DT646672

EST:     CAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: CAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG

EST: gi|76285053|gb|DV024621.1|DV024621

EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG

EST: gi|88748834|gb|DY532975.1|DY532975

EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG

EST: gi|71430589|gb|DR811639.1|DR811639

EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG

EST: gi|149067463|gb|EE157671.2|EE157671

EST:     ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAG                         GGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG
genomic: ATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACG

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: 39 (upstream exon), 21 (downstream exon)
Score: 3

TCTAGGGAGGTTCAACACGAAGGCGTGCGTGTCCAACGTCACCGTACGAGATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcc ... acctttgcagGGCGGGTCGGGGCTGGTGCAGGGCGTGAGGTTCTCGAACATCCAGGTCACGGAGGTGCAGACGCCCATCATGATAGACCAGTTCTACTGCGACAGGGCGA

Block sizes: 35 (upstream exon), 15 (downstream exon)
Score: 4

Block sizes: 45 (upstream exon), 41 (downstream exon)
Score: 5

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 10

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTAGGGAGGTTCAACACGAAGGCGTGCGTGTCCAACGTCACCGTACGAGATGTCAAGATGTTCAGGACAACGACGGGTGTCAGAATCAAGACATGGCAGgtacgccgcccgtacgtcagaataatgcagtagcaggcagcagcagcaggcctaataattactaataaacctttgcag

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