ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGTTGGTGGAAACAGAGACAAGATTCAGCAGAAGATAGTAAAGGAGAAGATAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgctgctatgtctaccttgctcctatgcattttgttcaaccagctttgtgttattgttaaaacctactgtttacggccatcactctaccattcgatctcataatgtttccattttttgtggataatcatcctgccatgatcatgtcatatttctcaacactgttatttatttcag

Basic information

species	Zea mays
transcript	GRMZM2G056355_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G056355_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g21620.1 (Oryza sativa), 5'ss of exon 6

TGTTGGTGGAAACAGAGACAAGATTCAGCAGAAGATAGTAAAGGAGAAGATAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct-gctatgtctaccttgctcctatgcattt---tgttcaaccagctttgtgtta-ttgttaaaacctac-tgtttacggccatcactctaccattcgatctcataatgtttccattttttgtggataatcatcctgccatgatcatgtcatatttctcaacactgttatttatttcag
|||||| |||||||| |||||  ||||||||||||| || |||||||| || ||||| ||  ||||||||||||| |||||||| ||  || | ||||| |||||||| | || | || | |  || | |   |||      | ||    |||| ||||| || ||  || |  | || |||||         | |  |   || |  |   | |||||||                                                                  
TGTTGGCGGAAACAGGGACAAAGTTCAGCAGAAGATTGTTAAGGAGAAAATTAAGCTTCCGGCATATTTATCTAGCGAAGTTCATTCTCTGCTAAAAGGCgtaagttgtttgccaagt-tgctatgattcaccgcacccatatttttttgcagccttgtgctagtttctagagtcaacctgtttgatcttgggattgaatttttagtccatcttatgtttcag----------------------------------------------------------------

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|71756320|gb|DR954257.1|DR954257

EST:     TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGA                         TTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT
genomic: TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT

EST: gi|16925331|gb|BM078399.1|BM078399

EST:     TANAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGA                         TTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT
genomic: TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT

EST: gi|211350193|gb|FL470898.1|FL470898

EST:     TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGA                         TTATTGCACAAAGAAGCTGGCAGAAGGCTGGGAAGCGGACCAGGCGGCAGT
genomic: TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT

EST: gi|5081127|gb|AI738173.1|AI738173

EST:     TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGA                         TTATTGCNCAAAGAAGCTGGCAGACGGCTGGGAAGCGGGCCAGGCGGCAGT
genomic: TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT

EST: gi|211042390|gb|FL284657.1|FL284657

EST:     AGTGAAGTTCATTCAATGTTGAAAGGA                         TTCTTGAAGAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT
genomic: AGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT

EST: gi|5740692|gb|AI948382.1|AI948382

EST:     TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGA                         TTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT
genomic: TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT

EST: gi|71444003|gb|DR825053.1|DR825053

EST:     TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGA                         TTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT
genomic: TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT

EST: gi|211042389|gb|FL284656.1|FL284656

EST:     TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGA                         TTATTGCACAAAGAWGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT
genomic: TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT

EST: gi|60348805|gb|DN215778.1|DN215778

EST:     TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGA                         TTATTGCACAAAGAAGCTGGCAGAAGGCTGGGAAGCGGACCAGGCGGCAGT
genomic: TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT

EST: gi|86466929|gb|DY233299.1|DY233299

EST:     TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGA                         TTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT
genomic: TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT

EST: gi|148942871|gb|EC887913.2|EC887913

EST:     TAAAGCTGCCAACATATTTATTTAGTGAAGTTCACTCAATGTTGAAAGGA                         TTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT
genomic: TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT

EST: gi|78107161|gb|DV525579.1|DV525579

EST:     TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGA                         TTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT
genomic: TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT

EST: gi|86465903|gb|DY232276.1|DY232276

EST:     TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGA                         TTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT
genomic: TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT

EST: gi|86470262|gb|DY236632.1|DY236632

EST:     TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGA                         TTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT
genomic: TAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGT

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: 48 (upstream exon), 49 (downstream exon)
Score: 132

TGTTGGTGGAAACAGAGACAAGATTCAGCAGAAGATAGTAAAGGAGAAGATAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgct ... tttatttcagTTATTGCACAAAGAAGCTGGCAGACGGCTGGGAAGCGGACCAGGCGGCAGTGACGAAATCAAGAACCACAAGTGGTTCAAGTCTGTAAACTGGAAGAGGC

Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 58

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 67

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGGTGGAAACAGAGACAAGATTCAGCAGAAGATAGTAAAGGAGAAGATAAAGCTGCCAACATATTTATCTAGTGAAGTTCACTCAATGTTGAAAGGAgtaagttgctgctatgtctaccttgctcctatgcattttgttcaaccagctttgtgttattgttaaaacctactgtttacggccatcactctaccattcgatctcataatgtttccattttttgtggataatcatcctgccatgatcatgtcatatttctcaacactgttatttatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC