ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CTTCCTCATAGTGAGAAAATGAAGCTTCTCCGAGACGAGAAGAATAGAGGGTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttattcaaactccacggttgttgctgcacataaatctagttttttcatgggccatctatggtagagagctgctagtgatgaaaaatcttgtcaag...

Basic information

species	Zea mays
transcript	GRMZM2G147882_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G147882_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 5'ss of exon 2

CTTCCTCATAGTGAGAAAATGAAGCTTCTCCGAGACGAGAAGAATAGAGGGTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaa-gttattcaaactccacggttgttgctgcacat--aaatctagttttttcatgggccatctatggtagagagctgctagtgatgaaaaatcttgtcaag
|||||    | |||||||||| |||||||||| || ||||||||| |||| || ||||||||||||||||| ||||||||||| ||||||||||| ||||||||   |||| ||   |  |   ||||| |    ||  ||||    | |  | |||  |   | ||  |   |   |     | || |  || ||  | || 
CTTCCCATCAATGAGAAAATGGAGCTTCTCCGGGATGAGAAGAATCGAGGCTATACACCCATGCTAGATGAGATTCTTGATCCAGAAAATCAAGTGAATGgtaataatatttaactcctgcatgtgttgtttattattaaaattgcatgtcatgatgtactgac-atactcttggttttgagattattagcaagct-attaa-

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|211501569|gb|FL375241.1|FL375241

EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTGAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC

EST: gi|32858736|gb|CD998417.1|CD998417

EST:     TACCACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTGAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: TA-CACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC

EST: gi|88756322|gb|DY540463.1|DY540463

EST:     GTACACACCCATGCTAGATGATATTCTTGATCCTGAGAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGCAGTTGAGGTACCTGCTGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC

EST: gi|74241070|gb|DT648984.1|DT648984

EST:     ACACACCCATGCTAGATGAAATTCCTTGATCCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: ACACACCCATGCTAGATGAAATTC-TTGATCC-TGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC

EST: gi|78117759|gb|DV536146.1|DV536146

EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC

EST: gi|78078284|gb|DV506699.1|DV506699

EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC

EST: gi|88756286|gb|DY540427.1|DY540427

EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC

EST: gi|93014970|gb|EB640490.1|EB640490

EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC

EST: gi|33466889|gb|CF243938.1|CF243938

EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGC

EST: gi|71299023|gb|DR785502.1|DR785502

EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC

EST: gi|71429426|gb|DR810476.1|DR810476

EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC

EST: gi|50323931|gb|CO519057.1|CO519057

EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC

EST: gi|211382338|gb|FL400551.1|FL400551

EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTGAATG                         GTGACTACAAGGAAGGATATTATATCGGAGTTGAGGTACCTGCA
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCA

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), 39 (downstream exon)
Score: 43

CTTCCTCATAGTGAGAAAATGAAGCTTCTCCGAGACGAGAAGAATAGAGGGTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATCCAGAAGCAAACAGGCCATTTTATGGTCCAAATCAGTGGCCTTCTAAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1299

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1071

Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 98

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCCTCATAGTGAGAAAATGAAGCTTCTCCGAGACGAGAAGAATAGAGGGTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttattcaaactccacggttgttgctgcacataaatctagttttttcatgggccatctatggtagagagctgctagtgatgaaaaatcttgtcaag

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