ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGCTTGCGATATAAATGAAGATATGGGCATGAAGTTCAACGAGTTCATTGTCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCAgtatccttcataagtcatattaattcacatagtaacatcctgattgcattattagtgttattgtcacattgtgttgtgttgctacagaggtatgcaatgt...

Basic information

species	Zea mays
transcript	GRMZM2G006790_T02
intron #	3
splice site	5'
intron type	U12 (go to U12 genes for details)

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G006790_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g40720.1 (Oryza sativa), 5'ss of exon 3

AGCTTGCGATATAAATGAAGATATGGGCATGAAGTTCAACGAGTTCATTGTCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCAgtatccttcataagtcatattaattcacatagtaacatcctgattgcattattagt--gttattgtcacattgtgttgtgttgctacagaggtatgcaatgt--
|||||| |||||||||||||| ||||||||||||||||| |||||||| ||||||||||||||  | ||||| ||||| ||| ||||||| |  ||||||||||||||        |          || || ||  |   | | |||| ||  ||  | |||||  | |   || |   || |||   |  | | | || |  
AGCTTGTGATATAAATGAAGACATGGGCATGAAGTTCAATGAGTTCATCGTCTTTCTGTGCCTCATTTATCTGCTCAACGAACCAGCTGTGTCAGAAGCAgtatccttttcttaataagcattgctgcagagcaatgttgggttagcat-ataggttaggtattgcaaaa--atgatacattactatttac-tgttctattttc

upper sequence: GRMZM2G006790_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv19s0015g01200.t01 (Vitis vinifera), 5'ss of exon 3

AGCTTGCGATATAAATGAAGATATGGGCATGAAGTTCAACGAGTTCATTGTCTTTCTGTGCCTTGTCTATCTTCTCAATGAAG---CAGCTGTCTTGGAAGCAgtatccttcataagtcatattaattcacatagtaacatcctgattgcattattagtgttatt-gtcacattgtgttgtgttgctacagaggtatgcaatgt---------
    || ||||| ||||| |||||||| ||||||||||| |||||||||||  |||| |||||||||||||||||||| || |   | |||| | |  | || ||||||     ||   | || ||||    || ||| ||  || || | |||  | || | ||  | || |  |      ||     |      ||  || |         
---ATGTGATATCAATGAGGATATGGGAATGAAGTTCAATGAGTTCATTGTACTTCTCTGCCTTGTCTATCTTCTCAAGGAGGATCCTGCTGCCCTTCAGGCCgtatcc-----aaagtacat-aatt----tattaatattttgtttcctttaaaaatgatgtttattacttcttacctaattcgcgaaacatattgtgatttaattgcagg

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|78112681|gb|DV531075.1|DV531075

EST:     TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCA                         AAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT
genomic: TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCAgtatccttca ... tacttcacagAAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT

EST: gi|211366893|gb|FL196958.1|FL196958

EST:     KCTTTCTGKGCCTTGKCTATCTTCTCAATGAAGCAGCTGTCTCGGAAGCA                         AAGATAAAGATGGGACTAGGAAA
genomic: TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCAgtatccttca ... tacttcacagAAGATAAAGATGGGACTAGGAAA

EST: gi|211062667|gb|FL265119.1|FL265119

EST:     TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCA                         AAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT
genomic: TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCAgtatccttca ... tacttcacagAAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT

EST: gi|60399811|gb|DN232621.1|DN232621

EST:     TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCA                         AAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT
genomic: TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCAgtatccttca ... tacttcacagAAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT

EST: gi|5928708|gb|AW055925.1|AW055925

EST:     TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCA                         AAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT
genomic: TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCAgtatccttca ... tacttcacagAAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT

EST: gi|40334046|gb|CK368116.1|CK368116

EST:     TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTCGGAAGCA                         AAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT
genomic: TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCAgtatccttca ... tacttcacagAAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT

EST: gi|60394800|gb|DN227670.1|DN227670

EST:     TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCA                         AAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT
genomic: TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCAgtatccttca ... tacttcacagAAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT

EST: gi|78086237|gb|DV514630.1|DV514630

EST:     TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCA                         AAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT
genomic: TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCAgtatccttca ... tacttcacagAAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT

EST: gi|74234337|gb|DT642251.1|DT642251

EST:     TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCA                         AAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT
genomic: TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCAgtatccttca ... tacttcacagAAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT

EST: gi|74234338|gb|DT642252.1|DT642252

EST:     CTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAAGCA                         A-GATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCG
genomic: CTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAA-GCAgtatccttca ... tacttcacagAAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCG

EST: gi|78112680|gb|DV531074.1|DV531074

EST:     TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCA                         AAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT
genomic: TCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCAgtatccttca ... tacttcacagAAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTT

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: 36 (upstream exon), 41 (downstream exon)
Score: 67

AGCTTGCGATATAAATGAAGATATGGGCATGAAGTTCAACGAGTTCATTGTCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCAgtatccttca ... tacttcacagAAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTTGATGCGTTTGTCTTCTTGGATAAGAATAAAGATGGGTATGTGAGCAAGG

Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 108

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 149

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1007

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTTGCGATATAAATGAAGATATGGGCATGAAGTTCAACGAGTTCATTGTCTTTCTGTGCCTTGTCTATCTTCTCAATGAAGCAGCTGTCTTGGAAGCAgtatccttcataagtcatattaattcacatagtaacatcctgattgcattattagtgttattgtcacattgtgttgtgttgctacagaggtatgcaatgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG