ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...gacttcaaacctatcactcgtactaccttcgtaaccctaattccaacacttacgtcagcagagcgagcagtaattgattgcatgctctattttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTCATCTAACCGTACAAAGGCAACACCGATCCAGTCCTCTAAGCAGGGTGTG

Basic information

species	Zea mays
transcript	GRMZM5G868908_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G868908_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g33180.1 (Oryza sativa), 3'ss of exon 3

-------------------------------------------------------gacttcaaacctatcactcgtac--taccttcgtaacc--ctaattccaacacttacgtcagcagagcgagcagtaattgattgcatgctctattttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTCATCTAACCGTACAAAGGCAACACCGATCCAGTCCTCTAAGCAGGGTGTG
                                                        |||     |     ||  | ||  |||| ||    |   |   ||       |||    | |  |||  | |   ||  || | ||||| || |   |||||| |||| ||| |||||||| ||||| || ||||||||||||||||| ||| |  |||| |   ||||||||   ||  ||||| | || |||||| |||||
gtaaggatccctctctagtatttccttttcacagcatgcacccacaacataagtcaactatgtgctatcaacctgaacattaccatctgggctggcctgttgtgtattttagcaaaaccaagcatgaatgcatgaatcgtatgctgtactgctgtgtagGTGCAAAACTGGAAAGCACACAACTGAGAAACCAATCACAAAAGCAGTTCCTACTAAACCATCAAAGGCAGTTCCAGTCCAGACTTCGAAGCAGAGTGTG

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|76281022|gb|DV020590.1|DV020590

EST:     TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGG                         ATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC
genomic: TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGGgtaaggaccc ... tttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC

EST: gi|76020023|gb|DT947193.1|DT947193

EST:     TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGG                         ATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC
genomic: TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGGgtaaggaccc ... tttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC

EST: gi|148956886|gb|EC902807.2|EC902807

EST:     TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGG                         ATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC
genomic: TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGGgtaaggaccc ... tttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC

EST: gi|89754532|gb|DY685280.1|DY685280

EST:     TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGG                         ATGCCCAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC
genomic: TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGGgtaaggaccc ... tttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC

EST: gi|211095546|gb|FL307582.1|FL307582

EST:     TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGG                         ATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC
genomic: TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGGgtaaggaccc ... tttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC

EST: gi|50332845|gb|CO527971.1|CO527971

EST:     TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGG                         ATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC
genomic: TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGGgtaaggaccc ... tttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC

EST: gi|50333184|gb|CO528310.1|CO528310

EST:     TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGG                         ATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC
genomic: TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGGgtaaggaccc ... tttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC

EST: gi|32910587|gb|CF015399.1|CF015399

EST:     TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGG                         ATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC
genomic: TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGGgtaaggaccc ... tttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC

EST: gi|76292110|gb|DV031678.1|DV031678

EST:     TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGG                         ATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC
genomic: TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGGgtaaggaccc ... tttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC

EST: gi|148930846|gb|EC873247.2|EC873247

EST:     TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGG                         ATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC
genomic: TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGGgtaaggaccc ... tttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC

EST: gi|211299419|gb|FL314583.1|FL314583

EST:     TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGG                         ATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC
genomic: TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGGgtaaggaccc ... tttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC

EST: gi|211166826|gb|FL324154.1|FL324154

EST:     TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGG                         ATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC
genomic: TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGGgtaaggaccc ... tttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC

EST: gi|9824964|gb|BE575061.1|BE575061

EST:     TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGG                         ATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC
genomic: TGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGGgtaaggaccc ... tttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTC

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: 47 (upstream exon), 49 (downstream exon)
Score: 73

CCTATGTTTCATGACGGCATGAAAGAATGGAGCTGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGGgtaaggaccc ... tttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTCATCTAACCGTACAAAGGCAACACCGATCCAGTCCTCTAAGCAGGGTGTG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 141

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 63

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

acacttacgtcagcagagcgagcagtaattgattgcatgctctattttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTCATCTAACCGTACAAAGGCAACACCGATCCAGTCCTCTAAGCAGGGTGTG

                                       ctctatttt  CT-rich tract
                         taattgatt  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacttcaaacctatcactcgtactaccttcgtaaccctaattccaacacttacgtcagcagagcgagcagtaattgattgcatgctctattttggtgtagATGCACAACAGGAAAGCATACAACCGAAAAACCAATCACAAAAGCTGTTTCATCTAACCGTACAAAGGCAACACCGATCCAGTCCTCTAAGCAGGGTGTG

- - - - - - - - - - - - - - - - - - - - - ccaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - tcagcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agcagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgc