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

gttatgccctttctcttcccttcttgctgtgcgaaacccagcaccatccgaaccctaacttgagctatctggctatttgcatccggatctgatctaattaccaagcgtgtacatacatactactaacttcgattttttttttgggaaaaatattggaacatccgtgtcctttaccgggttcccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGCAAGGCGGAGCGGAAAGCAGCACTAGATGCTGGCGCATGGATGTTCAATG

Basic information

species	Zea mays
transcript	GRMZM5G823629_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G823629_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 1

gttatgccctttctcttcccttcttgctgtgcgaaacccagcaccatccgaaccctaacttgagctatctggctatttgcatccggatctgatctaattaccaagcgtgtacatacatactactaacttcgattttttttttgggaaaaatattggaacatccgtgtcctttaccgggttcccccctatagAAAATTCGAGT---ATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGCAAGGCGGAGCGGAAAGCAGCACTAGATGCTGGCGCATGGATGTTCAATG------
                                                                                         || | || ||         ||||    |   |  | |      | || ||| |    ||| || | ||    |||  || | ||  |   |      |   ||   |||   |   |||  ||||||||||  ||||||||||||| |||| || ||| || ||| | |||||||  || |||||||| |||||||||||||| |      
-----------------------------------------------------------------------------------------tggtttattttg-------gtactagtagcttgttgatggacctcttatttatatctaaactaattga----ccgcatcttgtattgaactagtagtttctgatgcttcagATCGGATTGTACTCTACATGATAAGAAAGTATGGCACCAGCAAACAAAGCAGAGAGAAAAGCAGTGCTGGATGCTGGAGCATGGATGTTCAACGTTGTGA

upper sequence: GRMZM5G823629_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 3'ss of exon 1

gttatgccctttctcttcccttcttgctgtgcgaaacccagcaccatccgaaccctaacttgagctatctggctatttgcatccggatctgatctaattaccaagcgtgtacatacatactactaac-ttcgattttttttttgggaaaaatattggaacatccgtgtcctttaccgggttcccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGCAAGGCGGAGCGGAAAGCAGCACTAGATGCTGGCGCATGGATGTTCAATG
                                                                    || |  | | | ||     ||   | |  || | | | |  |  ||| || ||  ||   ||  | |  | | ||    |||||||       |   |    |  |  | | | | ||  |    ||||| ||   ||||| |||||||| ||||| |  ||||| || ||||||||||| ||| | ||||||||| ||||||||||                 
-------------------------------------------------------------------actagtgactcgtattgatttcacttgttttttctatgtgcatttatatatgcttatattattaaactcatgtcttaattaaaatat------gtttctaatgtagATTGTGATACTCCAAAATCCAAATTGGA---TTAGATTCTACATGACAAGAGAACATGGCACCTGGAAGCAAGGCAGAGAGAAAAGCAGCATTAGATGCTGGA----------------

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|78081629|gb|DV510041.1|DV510041

EST:     CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCA                         AAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC
genomic: CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCAgttatgccct ... ccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC

EST: gi|78079408|gb|DV507820.1|DV507820

EST:     CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCA                         AAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC
genomic: CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCAgttatgccct ... ccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC

EST: gi|211496862|gb|FL065359.1|FL065359

EST:     CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCA                         AAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC
genomic: CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCAgttatgccct ... ccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC

EST: gi|76280570|gb|DV020138.1|DV020138

EST:     CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCA                         AAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC
genomic: CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCAgttatgccct ... ccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC

EST: gi|211496860|gb|FL065357.1|FL065357

EST:     CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCA                         AAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC
genomic: CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCAgttatgccct ... ccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC

EST: gi|71445237|gb|DR826287.1|DR826287

EST:     CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCA                         AAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC
genomic: CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCAgttatgccct ... ccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC

EST: gi|76281274|gb|DV020842.1|DV020842

EST:     CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCA                         AAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC
genomic: CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCAgttatgccct ... ccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC

EST: gi|78111635|gb|DV530032.1|DV530032

EST:     CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCA                         AAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC
genomic: CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCAgttatgccct ... ccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC

EST: gi|50328555|gb|CO523681.1|CO523681

EST:     CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCA                         AAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC
genomic: CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCAgttatgccct ... ccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC

EST: gi|211496859|gb|FL065356.1|FL065356

EST:     CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCA                         AAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC
genomic: CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCAgttatgccct ... ccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC

EST: gi|211496857|gb|FL065354.1|FL065354

EST:     CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCA                         AAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC
genomic: CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCAgttatgccct ... ccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC

EST: gi|211496858|gb|FL065355.1|FL065355

EST:     CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCA                         AAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC
genomic: CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCAgttatgccct ... ccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC

EST: gi|91051408|gb|EB161826.1|EB161826

EST:     CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCA                         AAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC
genomic: CAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCAgttatgccct ... ccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGC

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: 45 (upstream exon), 46 (downstream exon)
Score: 29

GGTGCCCGAGCGTTCTCGTGCGGCAAGTGGGCGCCGCCGCCGGACTACGCCAGGTGCCCAGTTCCTCGTCGGGTCCTTCGTCGACGACGAGCACCCACCAgttatgccct ... ccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGCAAGGCGGAGCGGAAAGCAGCACTAGATGCTGGCGCATGGATGTTCAATG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 40

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 22

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 70

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgggaaaaatattggaacatccgtgtcctttaccgggttcccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGCAAGGCGGAGCGGAAAGCAGCACTAGATGCTGGCGCATGGATGTTCAATG

                                          ttcccccctat  CT-rich tract
         aaaaatatt  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatgccctttctcttcccttcttgctgtgcgaaacccagcaccatccgaaccctaacttgagctatctggctatttgcatccggatctgatctaattaccaagcgtgtacatacatactactaacttcgattttttttttgggaaaaatattggaacatccgtgtcctttaccgggttcccccctatagAAAATTCGAGTATTAGACTCTACATGTCAAGAAAGTATGGCGCCAGGAAGCAAGGCGGAGCGGAAAGCAGCACTAGATGCTGGCGCATGGATGTTCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA