ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtattcagttcatatcttctccatcctaccctgcctggctgaacgtctgaacctgaacgccttcgcctactgcacgatgtcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCATCACTCTCTCTCTCGATAGAGTTGCCGCATCTGCGCTCAAAGATGTCAT

Basic information

species	Zea mays
transcript	GRMZM5G824597_T02
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G824597_T02 (Zea mays), 3'ss of exon 2
lower sequence: 13113.m00164 (Oryza sativa), 3'ss of exon 2

gtattcagttcatatcttctccatcctaccctgcctggctgaacgtctgaacctgaacgccttcgcc-tactgcacgatgtcgta-tgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCATCACTCTCTCTCTCGATAGAGTTGCCGCATCTGCGCTCAAAGATGTCAT
    || || |  |   |  | || | || ||   |  |   ||     |   ||  |  |||| |  | ||        |  || | |||| | ||||   | | | ||||| ||||| ||||||||||| ||||||||||||||  | || ||| | |   || |    || ||||| || ||||||||
---gtcggtactcaaactacctataccacgcttttttacactacactaca--ttgcccatcttccctatgctcatatggataatactacagGGCTTGATCGCGTTCATCTTGTTGCTACAAAGGCAAAGGGTCTACCTCGCATCACCATTTCCCTCAACACCCTTACTCACTCCGCGCTGAATGATGTCAT

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|211495258|gb|FL115225.1|FL115225

EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

EST: gi|94476029|gb|EB704987.1|EB704987

EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTGGTGGCTACCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCA

EST: gi|211495257|gb|FL115224.1|FL115224

EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

EST: gi|94479640|gb|EB708598.1|EB708598

EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

EST: gi|211495259|gb|FL115226.1|FL115226

EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

EST: gi|94476028|gb|EB704986.1|EB704986

EST:     CCGCGGCCCTAG                         GTCCTGATTCTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: CCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

EST: gi|211498135|gb|FL115228.1|FL115228

EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

EST: gi|166453393|gb|EG139875.1|EG139875

EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

EST: gi|211498137|gb|FL115230.1|FL115230

EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

EST: gi|211498138|gb|FL115231.1|FL115231

EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

EST: gi|211498134|gb|FL115227.1|FL115227

EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

EST: gi|211498136|gb|FL115229.1|FL115229

EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

EST: gi|94476020|gb|EB704978.1|EB704978

EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

EST: gi|94479639|gb|EB708597.1|EB708597

EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

EST: gi|76283433|gb|DV023001.1|DV023001

EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

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), 48 (downstream exon)
Score: 31

GACGTTGGCATCGCTGGCTCCTGCTCCGACTTCCTCGACTACCTCTATTCTTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCATCACTCTCTCTCTCGATAGAGTTGCCGCATCTGCGCTCAAAGATGTCAT

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

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

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 27

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcagttcatatcttctccatcctaccctgcctggctgaacgtctgaacctgaacgccttcgcctactgcacgatgtcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCATCACTCTCTCTCTCGATAGAGTTGCCGCATCTGCGCTCAAAGATGTCAT

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