ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTTTGACATGCTGCGTAGACAGTCCCTCCGCCCTGATAACATCAAGATGTTTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacacttctattttatttctattctctctatgcttgatcatggtacctgtattctttgctagtaaagtgcagagattaagtttaaattgatttgcca...

Basic information

species	Zea mays
transcript	GRMZM2G027995_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G027995_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g48750.1 (Oryza sativa), 5'ss of exon 4

GTTTGACATGCTGCGTAGACAGTCCCTCCGCCCTGATAACATCAAGATGTTTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacact-tctattttatttctattctctctatgcttga-----tcatggtacctgtattctttgctagtaaagtgcagagattaagtttaaattgatttgcca
|||||||||||||||||| ||||||||||| |||||| |||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||||| | || | |||   || ||| |||| |   | || ||       | |   ||  |  | | | ||  || |   | ||   || |   |  ||||  |      
GTTTGACATGCTGCGTAGGCAGTCCCTCCGTCCTGATTACATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgttagcattatcttagttgtttgtattttgcatttggtttgcggtttaacactatttagactttctgagagcatgattcattaatgattgtacaattctt------

upper sequence: GRMZM2G027995_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3

GTTTGACATGCTGCGTAGACAGTCCCTCCGCCCTGATAACATCAAGATGTTTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacacttctattttatttctattctctctatgcttgatcatggtacctgtattctttgctagtaaagtgcagagattaagtttaaattgatttgcca
 |  || |||||  |  | |   | || || || ||  |||||||||||||||| || ||||| || || || ||||| || || ||||||||||| |||||||          |  |     |     |||||   | | ||   | |||||    | || |     ||                              
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaa--------ggtggaaggaaagctggtctata--taaccaccctgcctgtgccttgtg-tgtcgcag------------------------------

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|32928681|gb|CF033493.1|CF033493

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|31354357|gb|CD438714.1|CD438714

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|33091564|gb|CF051558.1|CF051558

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|67041361|gb|CO467616.1|CO467616

EST:     TTGTTCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|20300961|gb|BQ163904.1|BQ163904

EST:     TTGTTCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|67031983|gb|CO460732.1|CO460732

EST:     TTGTTCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|31359591|gb|CD443948.1|CD443948

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|31354677|gb|CD439034.1|CD439034

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|32928895|gb|CF033707.1|CF033707

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|31351797|gb|CD436154.1|CD436154

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|67015597|gb|CO444346.1|CO444346

EST:     TTGTTCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|31359138|gb|CD443495.1|CD443495

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTT-CAAGGATCAG                         ATTTATGACATCTT
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTT

EST: gi|32847017|gb|CD986698.1|CD986698

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|32856210|gb|CD995891.1|CD995891

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|33092615|gb|CF052609.1|CF052609

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|32849501|gb|CD989182.1|CD989182

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|51592787|gb|CV071933.1|CV071933

EST:     TTGTTCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|13178108|gb|BG349366.1|BG349366

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATCTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|166694651|gb|EG210441.1|EG210441

EST:     ATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTA
genomic: ATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTT-

EST: gi|29946169|gb|CB816014.1|CB816014

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGGGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCT
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCT

EST: gi|32910618|gb|CF015430.1|CF015430

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|211288100|gb|FL159903.1|FL159903

EST:     TTGTTCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|31356525|gb|CD440882.1|CD440882

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|31349540|gb|CD433897.1|CD433897

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|19272583|gb|BM888839.1|BM888839

EST:     TTGTTCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|31353577|gb|CD437934.1|CD437934

EST:     TTGTTCTTGACGAACCTGATGAAATGCTTTCTCGTGGTTTCAAAGATCAG                         ATTTATGACATCTTCCAGCTTCTGGCCATCCAAGATTCAGGTT
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTG-CCATCCAAGATTCAGGTT

EST: gi|67017759|gb|CO446508.1|CO446508

EST:     TTGTTCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

EST: gi|60400475|gb|DN233282.1|DN233282

EST:     TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAG                         ATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC
genomic: TTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTC

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: 848

GTTTGACATGCTGCGTAGACAGTCCCTCCGCCCTGATAACATCAAGATGTTTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacactt ... tggaatgcagATTTATGACATCTTCCAGCTTCTGCCATCCAAGATTCAGGTTGGAGTCTTCTCTGCTACCATGCCACCTGAGGCCCTTGAGATTACCCGCAAGTTCATGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 773

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 724

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 486

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGACATGCTGCGTAGACAGTCCCTCCGCCCTGATAACATCAAGATGTTTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacacttctattttatttctattctctctatgcttgatcatggtacctgtattctttgctagtaaagtgcagagattaagtttaaattgatttgcca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT