ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ACAAGAGTAGCTCTTAACAATCAGAGGGCCATGTTTGGAGACATTCAAGGGAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTGgtaatatattgatcccttctctgccgccgcaggccgcagcactgatttcttgtcatgctggcatcgtattgctcactgctgtgtgacgctacatccatatataattatgcctaatccgcccttgcag

Basic information

species	Zea mays
transcript	GRMZM5G838961_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G838961_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g03450.1 (Oryza sativa), 5'ss of exon 4

ACAAGAGTAGCTCTTAACAATCAGAGGGCCATGTTTGGAGACATTCAAGGGAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTGgtaatatattgatcccttctctgccgccgcaggccgcagcactgatttcttgtcatg--ctggcatcgtatt------gctca-ctgctgtgtgacgctacatccatatat-aattatgcctaatc-cgccc-ttgcag----------------------------------------------------
||||| ||||| |||  ||||||||||||  ||||||| ||  ||||||| ||||| |||||| |||||||||||||||| || || ||||| || ||||||||| |||  |||||   | | |      |     |    || |  | ||||  ||  ||||||| ||  |      ||| | ||  | |    ||  |  ||   ||   || | | | | |||  |    ||  ||                                                    
ACAAGGGTAGCCCTTTCCAATCAGAGGGCATTGTTTGGGGATGTTCAAGGAAAAGTCAAGCAGTTGGGTGAAAAGTTCCCTGTTATTAGAGGACTACTTGgtaatgtatcaatccccaatttacatttttattgatcctttcttacatattgttctgaactggcattgtgctaaatgtgctaatctattattcaccgaaatttctgcatcccaactttccatgatcatgtttgttttagtttgtgttagtagttagtacaccactacctttcttacacattcttgctacag

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|67024939|gb|CO453688.1|CO453688

EST:     GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTG                         GTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA
genomic: GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTGgtaatatatt ... gcccttgcagGTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA

EST: gi|5670923|gb|AI932186.1|AI932186

EST:     GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTG                         GTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA
genomic: GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTGgtaatatatt ... gcccttgcagGTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA

EST: gi|78125718|gb|DV544102.1|DV544102

EST:     GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTG                         GTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA
genomic: GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTGgtaatatatt ... gcccttgcagGTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA

EST: gi|211007692|gb|FL462067.1|FL462067

EST:     GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTG                         GTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA
genomic: GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTGgtaatatatt ... gcccttgcagGTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA

EST: gi|71758975|gb|DR956912.1|DR956912

EST:     GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTG                         GTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA
genomic: GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTGgtaatatatt ... gcccttgcagGTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA

EST: gi|76017094|gb|DT944264.1|DT944264

EST:     GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTG                         GTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA
genomic: GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTGgtaatatatt ... gcccttgcagGTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA

EST: gi|211238072|gb|FL481633.1|FL481633

EST:     GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTG                         GTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA
genomic: GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTGgtaatatatt ... gcccttgcagGTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA

EST: gi|76011973|gb|DT939143.1|DT939143

EST:     GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTG                         GTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA
genomic: GAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTGgtaatatatt ... gcccttgcagGTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGA

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), 45 (downstream exon)
Score: 36

ACAAGAGTAGCTCTTAACAATCAGAGGGCCATGTTTGGAGACATTCAAGGGAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTGgtaatatatt ... gcccttgcagGTGCCATCAAGCGGAAGAAATCAAAGGACACCATAATCCTCTCGGCAGTGATCGCGGCCTGCACCATCTTCCTGATCATTTACTGGCTTTCGAAATGATG

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 45

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

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 21

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAAGAGTAGCTCTTAACAATCAGAGGGCCATGTTTGGAGACATTCAAGGGAAAGTGAAGCAGCTGGGTGAAAAGTTCCCGGTAATCAGAGGTCTTCTTGgtaatatattgatcccttctctgccgccgcaggccgcagcactgatttcttgtcatgctggcatcgtattgctcactgctgtgtgacgctacatccatatataattatgcctaatccgcccttgcag

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