ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGGGGGATACATTGCTGGAGTATTCTGCGCGGCTATATCTCATCCTGCAGACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttctagtcctatctcagaataaaaaaataaaaatttcaaggctgaaaaatctgtcaccagtcgcactcacggaagagcctctgacaataggtttgtctaatttttggcttctaaccatttcaccatacatccag

Basic information

species	Zea mays
transcript	GRMZM2G118208_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G118208_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g15690.2 (Oryza sativa), 5'ss of exon 3

AGGGGGATACATTGCTGGAGTATTCTGCGCGGCTATATCTCATCCTGCAGACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttctagtcctatctcagaataaaaaaataaaaatttcaaggctgaaaaatctgtcaccagtcgcactcacggaagagcctctgacaataggtttgtctaatttttggcttctaaccatttcaccatacatccag
||||||||| ||||| ||||| ||||| || ||||| |||||||||||||||||||| || |||||||| ||||||||||| || | |||  |||| |||||||||| |||| ||| ||   || |   | |  |||||           |||  |||  ||||    |   ||| | ||    ||     | |   ||||| ||| | ||    ||| |||| | ||    || | |||
AGGGGGATATATTGCAGGAGTCTTCTGTGCAGCTATCTCTCATCCTGCAGACAACCTGGTGTCTTTCCTCAACAATGCAAAGGGGGGCACTATGGCTGATgtaagctgctagccctctcagtgactttcatataaaaaa-----------aaagttcttacacctactg---tcaagtaatgttct-----actgattttgtttaactatt----tctgaccaatgcattgcactttcag

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|211414538|gb|FL447526.1|FL447526

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|60347958|gb|DN214931.1|DN214931

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|71759052|gb|DR956989.1|DR956989

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|76281616|gb|DV021184.1|DV021184

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|101382650|gb|EB813379.1|EB813379

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTTCCTCT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTT-CCTCT

EST: gi|211372685|gb|FL440590.1|FL440590

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCGCCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATGTGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|74245908|gb|DT653822.1|DT653822

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|71417465|gb|DR804063.1|DR804063

EST:     ACAACCTTGTATTTTTCCTGAACAATGCAAATGGAGCCCCCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACCCGCGGCCTTCCTTTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|71426615|gb|DR807665.1|DR807665

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|71767405|gb|DR965342.1|DR965342

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|211162309|gb|FL458141.1|FL458141

EST:     TCTTTCCTGAACAATGCAAATGGAGCCMCCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: TCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|166422024|gb|EG308358.1|EG308358

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTG
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTG

EST: gi|6056814|gb|AW091219.1|AW091219

EST:     GTATCTTTCCTGACCAATGCAAAT-GAGCC-CCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: GTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|78024338|gb|DV492725.1|DV492725

EST:     CCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATGTGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: CCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|60354997|gb|DN221970.1|DN221970

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|37398965|gb|CF636804.1|CF636804

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|91874482|gb|EB404439.1|EB404439

EST:     ACAACCTCGTATCTTTCTTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|78544938|gb|DV622436.1|DV622436

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCGCCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATGTGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|60354455|gb|DN221428.1|DN221428

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|5108094|gb|AI739807.1|AI739807

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCGCCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATGTGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|67010579|gb|CO439328.1|CO439328

EST:     ACAACCTCGTATCTTTCCTGAACAATGCANATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATGTGGGGTCTTTTCACACGCGGCCTTNCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

EST: gi|166430911|gb|EG191663.1|EG191663

EST:     ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATAT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATAT

EST: gi|37381517|gb|CF627652.1|CF627652

EST:     ACAACCTCGTATCTTTCTTGAACAATGCAAATGGAGCCACCGTGGCAGAT                         GCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT
genomic: ACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTT

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), 47 (downstream exon)
Score: 50

AGGGGGATACATTGCTGGAGTATTCTGCGCGGCTATATCTCATCCTGCAGACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttct ... atacatccagGCTGTAAGAACTCTTGGAATATGGGGTCTTTTCACACGCGGCCTTCCTCTTCGTATAATTATGGTTGGTACTCTCACAGGAGCGCAATGGGCAGCCTATG

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 66

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 11

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGGGATACATTGCTGGAGTATTCTGCGCGGCTATATCTCATCCTGCAGACAACCTCGTATCTTTCCTGAACAATGCAAATGGAGCCACCGTGGCAGATgtaagcttctagtcctatctcagaataaaaaaataaaaatttcaaggctgaaaaatctgtcaccagtcgcactcacggaagagcctctgacaataggtttgtctaatttttggcttctaaccatttcaccatacatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT