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

gtagattccgctccattcgccgccaccgtcgtcaacaccgacgcgggcgttcaaatcatctgctcccgatcccatcccgtcatcagctcatctgtgggacctcatttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCTCTTCAGTGCTGCGCGGCGGTGGCGGGGGCTGGGAAGGGCCTGAGGTGAG

Basic information

species	Zea mays
transcript	GRMZM5G892742_T04
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G892742_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g25210.1 (Oryza sativa), 3'ss of exon 1

----gtagatt-ccgctccattcgccg-ccaccgtcgt-caacaccgacgcgggcgttcaaatcatctgctcccgatcccatcccgtcatcagc-tcatct-gtgggacctcatttc-tgcagCCGCGGC------GGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCTCTTCAGTGCTGCGCGGCGGTGGCGGGGGCTGGGAAGGGCCTGAGGTGAG
    |   | | || |  | ||||||| || || |||| |    ||    |   | ||  |  |  |  |||  ||||   || |     | || || | | || | |   | || | |||||| ||||       | | | ||| ||||| |||||||||| ||||||||| |||| ||| || | |||||||||||| || || ||  | | |||    |       
gtaggcgtactgccaccgccttcgccgtccgccctcgttctctccccgatcccccatttcaggctccgtctcgtgatcgtctcaccctgcctgcctcgtttcgtcgaattccgttccctgcagCGGCGGAACATCAGCATCAGCACCAGCAGCAGTACCAGTACCTGGGCCGCAGCAGCTCGTCGGCGCTGCGCGGCGGCGGTGGCGGAGGAGGAGGAGGAGC------

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|101401378|gb|EB822366.1|EB822366

EST:     GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAG                         CCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT
genomic: GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAGgtagattccg ... atttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT

EST: gi|71439824|gb|DR820874.1|DR820874

EST:     GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAG                         CCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT
genomic: GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAGgtagattccg ... atttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT

EST: gi|71438689|gb|DR819739.1|DR819739

EST:     GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAG                         CCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT
genomic: GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAGgtagattccg ... atttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT

EST: gi|148999746|gb|EE036749.2|EE036749

EST:     GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAG                         CCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT
genomic: GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAGgtagattccg ... atttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT

EST: gi|71438626|gb|DR819676.1|DR819676

EST:     GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAG                         CCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT
genomic: GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAGgtagattccg ... atttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT

EST: gi|71422780|gb|DR805839.1|DR805839

EST:     GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAG                         CCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT
genomic: GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAGgtagattccg ... atttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT

EST: gi|211426297|gb|FL054605.1|FL054605

EST:     GCGCGACGGCGAGGAGCAACGCCGCCTCCTCCTCTCCTCCACCCCGCCAG                         CCGCGGCGGACCTGCAGCAGCAGCAGTACCAGTTCCTGGGCCGGAGCACCT
genomic: GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAGgtagattccg ... atttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT

EST: gi|211426296|gb|FL054604.1|FL054604

EST:     CGCGACGGCGAGGAGCAACGCCGCCCCGCTCCTCTCCTCCACCCCGCCAG                         CYGCGGCGNACCCGCAGCAGCAGCAGTACCAGTTCCTGGGCCGGAGCACCT
genomic: CGCGACGGCGAGGAGCAACGCCGCCCC-CTCCTCTCCTCCACCCCGCCAGgtagattccg ... atttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT

EST: gi|76014459|gb|DT941629.1|DT941629

EST:     GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAG                         CCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT
genomic: GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAGgtagattccg ... atttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT

EST: gi|71446190|gb|DR827240.1|DR827240

EST:     GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAG                         CCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT
genomic: GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAGgtagattccg ... atttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT

EST: gi|76285537|gb|DV025105.1|DV025105

EST:     GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAG                         CCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT
genomic: GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAGgtagattccg ... atttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT

EST: gi|101387480|gb|EB815755.1|EB815755

EST:     GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAG                         CCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT
genomic: GCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAGgtagattccg ... atttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCT

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: 42 (upstream exon), 49 (downstream exon)
Score: 43

GTCCTCCCCCGACCAAACACAGTCCCTGGATCCATGGGTGTCGAGGAGGAGCGCGACGGCGAGGAGCAACGCCGCCCCCTCCTCTCCTCCACCCCGCCAGgtagattccg ... atttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCTCTTCAGTGCTGCGCGGCGGTGGCGGGGGCTGGGAAGGGCCTGAGGTGAG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 187

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 187

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tctgctcccgatcccatcccgtcatcagctcatctgtgggacctcatttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCTCTTCAGTGCTGCGCGGCGGTGGCGGGGGCTGGGAAGGGCCTGAGGTGAG

                                         cctcatttct  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagattccgctccattcgccgccaccgtcgtcaacaccgacgcgggcgttcaaatcatctgctcccgatcccatcccgtcatcagctcatctgtgggacctcatttctgcagCCGCGGCGGACCCGCAGCAGCAACAGTACCAGTTCCTGGGCCGGAGCACCTCTTCAGTGCTGCGCGGCGGTGGCGGGGGCTGGGAAGGGCCTGAGGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC