ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGATAACGGAGGAGGAACTACGGCAGTACGACGGGTCCGACCCCGAGAAACCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcctttgaatccttgattgcttcagtcctaacctttaattattcatccatttcgtcctaatcgcaactcgcagagctgctgtgctctgttgtac...

Basic information

species	Zea mays
transcript	GRMZM5G856734_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G856734_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g35850.1 (Oryza sativa), 5'ss of exon 2

AGATAACGGAGGAGGAACTACGGCAGTACGACGGGTCCGACCCCGAGAAACCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcctttgaatccttgattgcttcagtcctaacctttaa-ttattcatccatttcgtc-ctaatcgcaactcgcagagctgctgtgctctgttgtac
|||| |||| ||||||  | | ||||||||||||||||||||||||||| ||| |||| ||||| ||||||||||||||||||||||||||  ||||||||| |||| | || |  ||| | ||   | |  |||    || ||  | |||  | | |  ||  ||| |  |||    || |||||   ||     ||||  
AGATCACGGCGGAGGAGTTGCTGCAGTACGACGGGTCCGACCCCGAGAAGCCGTTGCTCATGGCGATCAAGGGGCAGATCTATGACGTCTCCCAGAGCAGgtcgctttcgttaagccctagcttctgtaaaccctcgttttaaagcttttctgctactatgtttctagtttcaaaaaccaaagctgaattgtggatttgt--

upper sequence: GRMZM5G856734_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ25427 (Selaginella moellendorffii), 5'ss of exon 1

AGATAACGGAGGAGGAACTACGGCAGTACGACGGGTCCGACCCCGAGAAACCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcctttgaatccttgattgcttcagtcctaacctt-taattattcatccatttcgtcctaatcgcaactcgcagagctgctgtgctctgttgtac
|| | ||||| ||||| ||  |    ||||| ||    ||   |   || |||||||| |||||||||||||| || ||||||||||||||   |  ||||| |      ||   | |   ||| | |  || | |    | | ||  ||     |||||                                         
AGGTCACGGAAGAGGAGCTCAGCGCCTACGATGGCAAGGATGACTCCAAGCCGCTGCTCATGGCCATCAAGGGCCAAATCTATGACGTCTCCATGTCCAGgtagaagagattc--ttccccatttcgtttgtgccactggtgtgatctttgggagatttcag---------------------------------------

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|211236490|gb|FK950766.1|FK950766

EST:     CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAG                         GATGTTCTATGGA
genomic: CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcct ... ccctgtgcagGATGTTCTATGGA

EST: gi|211237681|gb|FL238796.1|FL238796

EST:     CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAG                         GAAGTTCTATGGACCT
genomic: CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcct ... ccctgtgcagGATGTTCTATGGACCT

EST: gi|148986679|gb|EE030460.2|EE030460

EST:     CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAG                         GATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC
genomic: CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcct ... ccctgtgcagGATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC

EST: gi|71442989|gb|DR824039.1|DR824039

EST:     CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAG                         GATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC
genomic: CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcct ... ccctgtgcagGATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC

EST: gi|32845156|gb|CD984837.1|CD984837

EST:     CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAG                         GATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC
genomic: CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcct ... ccctgtgcagGATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC

EST: gi|29576888|gb|CB617000.1|CB617000

EST:     CGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAG                         GATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC
genomic: CGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcct ... ccctgtgcagGATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC

EST: gi|29544876|gb|CB605484.1|CB605484

EST:     CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAG                         GATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC
genomic: CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcct ... ccctgtgcagGATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC

EST: gi|148941737|gb|EC886692.2|EC886692

EST:     CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAG                         GATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC
genomic: CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcct ... ccctgtgcagGATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC

EST: gi|211086167|gb|FL437475.1|FL437475

EST:     CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAG                         GATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC
genomic: CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcct ... ccctgtgcagGATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC

EST: gi|211237687|gb|FL238802.1|FL238802

EST:     C-GCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAG                         GATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCT
genomic: CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcct ... ccctgtgcagGATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCT

EST: gi|149103627|gb|EE289029.2|EE289029

EST:     CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAG                         GATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC
genomic: CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcct ... ccctgtgcagGATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC

EST: gi|211235445|gb|FL238783.1|FL238783

EST:     CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAG                         GATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC
genomic: CCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcct ... ccctgtgcagGATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGC

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), 49 (downstream exon)
Score: 89

AGATAACGGAGGAGGAACTACGGCAGTACGACGGGTCCGACCCCGAGAAACCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcct ... ccctgtgcagGATGTTCTATGGACCTGGCGCAGCTTATGCTCTGTTTGCTGGTAAAGATGCCAGTAGGGCATTGGCTAAGATGTCCTTTGAATCACAGGATCTGAATGGT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 403

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATAACGGAGGAGGAACTACGGCAGTACGACGGGTCCGACCCCGAGAAACCGCTGCTGATGGCCATCAAGGGGCAGATCTATGACGTCTCAGAGAGCAGgttgcttcctttgaatccttgattgcttcagtcctaacctttaattattcatccatttcgtcctaatcgcaactcgcagagctgctgtgctctgttgtac

- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG