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

...gcatgtcgaaatgatctgcatattttgaaggaaggttgaaaggtcgatcattcatgtgctgttgtaagctgaccctgtgaattgggcgaattgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCTGGGATGGTGGGCGGCATGCTGCTCCACCTGCGCTCACTCCGCCGCTTCG

Basic information

species	Zea mays
transcript	GRMZM2G125669_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G125669_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g51150.1 (Oryza sativa), 3'ss of exon 2

gcatgtcgaaatgatctgca-tattttgaaggaagg----ttgaaaggtcgatcattcatgtg-ctgttgtaagctgaccctgtgaattgggcgaattgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCTGGGATGGTGGGCGGCATGCTGCTCCACCTGCGCTCACTCCGCCGCTTCG
  |  |   |   || |  | || | ||  | || |     |    ||||| | |||  |||  ||||     | | || |||  |||||||    |||  |||||||| ||||||||||||| |||||||||||||| || ||||| |||||||| ||||||||||||||||||||||||||||| || || ||||| |||||||
--acatgatatccatttctagtagtatgtggaaatgatctctagtcggtcgctaattgctgtaactgtcaatggttaacactgcaaattggg----ttgggtgcagAGGAGGTATGGCTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTCCACCTCCGGTCCCTCCGGCGCTTCG

upper sequence: GRMZM2G125669_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G14800.2 (Glycine max), 3'ss of exon 2

gcatgtcgaaatgatctgcatattttgaaggaaggttgaaaggtcgatcattcatgtg----ctgttgtaagct-gaccctgtgaattgggcgaattgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCTGGGATGGTGGGCGGCATGCTGCTCCACCTGCGCTCACTCCGCCGCTTCG
     | | | |  |         ||  | ||   ||| |   |  ||  |   | ||     | || |   ||  |    ||   ||| | | |       |||||||| ||||| ||||| || |||||||| ||||| |||||||| || ||||||||||| |  |||||||| || |||      || ||  |  | || |
-----ttgcagtacttgttcacccttagatgagtattgtattctatatactatgtttgaagtttattattttcttaattaagtttgttgtgtgtaaatgtaacagAGGCGATATGGATGCCGAGCAATGATGCTAGAAACAGTGGCTGCAGTCCCTGGGATGGTAGCAGGCATGCTACTTCACTGCAAATCCCTAAGAAGATTTG

upper sequence: GRMZM2G125669_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S183_11V6.1 (Physcomitrella patens), 3'ss of exon 3

gcatgtcgaaatgatctgcatattttgaaggaaggttgaaaggtcgatcattcatgtgctgttgtaagctgaccctgtgaattgggcgaattgtctgc------agAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCTGGGATGGTGGGCGGCATGCTGCTCCACCTGCGCTCACTCCGCCGCTTCG
  | |    ||     | || | || |  || |   | |    |   ||          | |||| |  ||    |  ||||     | ||| | |||      ||| ||||||||     || || ||||||||||| |||||||| || || ||||| ||||| ||||| |||||||||||       ||| | ||    ||  
-taggctataactgg-tacaaagttcgtcggga---ttagttttgtctcgagtgcagtttattgtca-ttggaattaggaatctcatgtattatttgctctcgcagAAGCGGTATGATGTTCGTGCAATGATGCTGGAGACCGTGGCGGCTGTTCCTGGAATGGTCGGCGGAATGCTGCTCCATTGCAAATCATTGCGTAAATTTC

upper sequence: GRMZM2G125669_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ27318 (Selaginella moellendorffii), 3'ss of exon 2

------------------------------------------------------------------gcatgtcgaa-atga-tctgcatattt-tgaaggaaggttgaaaggtc------gatcattcatgtgctgttgtaagctgaccctgtgaa-ttgggcgaattgt----ctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCTGGGATGGTGGGCGGCATGCTGCTCCACCTGCGCTCACTCCGCCGCTTCG
                                                                     | | ||| |||| |  |||| ||| ||  | |   |||  | ||       |||||  |  ||  | | ||  |||   | | | || |||| |  ||| |     ||||| | || || |||||||| ||||||||||| || || || |||||||| || |||||||| || || |||||||| |||   ||||| || ||||| ||||
gtgaaagcgatgcgtttgcccacagacattttcttccaggcaagatatctttctttctttctttctatcttttgaatatgaatgagcatgtttatgttgaatccttgcgaagttcctggggatcaaacgagt-ttttagtttgctagtcttataaacttggactgattttatttttgcagCGACGATACGGCTGCCGAGCGATGATGCTCGAGACTGTCGCTGCGGTCCCGGGGATGGTCGGGGGGATGCTGCTGCACTGCCGCTCGCTTCGCCGGTTCG

upper sequence: GRMZM2G125669_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ26025 (Selaginella moellendorffii), 3'ss of exon 3

gcatgtcgaaatgatctgcatattttgaaggaaggttgaaaggtcgatcattcatgtgctgttgtaagctgaccctgtgaattgggcgaattgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCTGGGATGGTGGGCGGCATGCTGCTCCACCTGCGCTCACTCCGCCGCTTCG
                              | | | |   | | |||   ||  | | || ||   || |||   | |||  |    |||   ||   ||||| ||||||| |||||||| ||||||||||| || |||||||  || || ||||||||||| ||||||||  | |||      ||  | ||||| ||||
------------------------------gtatgctcgcatggcgaattttttttttctctt---agttgatggtttgatctt--tgaa---tccaaagAGGAGGTATGGATGCCGGGCTATGATGCTGGAGACTGTGGCTGGAGTTCCCGGGATGGTGGGTGGCATGCTCTTGCACTGCAAATCCTTGCGCCGATTCG

upper sequence: GRMZM2G125669_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ14430 (Selaginella moellendorffii), 3'ss of exon 2

gcatgtcgaaatgatctgcatattttgaaggaaggttgaaaggtcgatcattcatgtgctgttgtaagctgaccctgtgaattgggcgaattgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCTGGGATGGTGGGCGGCATGCTGCTCCACCTGCGCTCACTCCGCCGCTTCG
                             | | | | | | ||   |   ||  | | || ||   || |||   | |||  |    |||   ||   ||||| |||| || |||||||| ||||||||||| || |||||||  || || ||||||||||| ||||||||  | |||      ||  | ||||| ||||
-----------------------------gtatgctcgcatggcgaaattttttttttctctt---agttgatggtttgatctt--tgaa---tccaaagAGGAGGTACGGATGCCGGGCTATGATGCTGGAGACTGTGGCTGGAGTTCCCGGGATGGTGGGTGGCATGCTCTTGCACTGCAAATCCTTGCGCCGATTCG

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|148933362|gb|EC877026.2|EC877026

EST:     CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAG                         AGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT
genomic: CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAGgttcgtgccc ... ttgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT

EST: gi|148947765|gb|EC893251.2|EC893251

EST:     CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAG                         AGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT
genomic: CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAGgttcgtgccc ... ttgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT

EST: gi|211472275|gb|FL205293.1|FL205293

EST:     CATACTGGACCGTCAAGTCGCTGCGTTTCCCCACGGACATCTTCTTCCAG                         AGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT
genomic: CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAGgttcgtgccc ... ttgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT

EST: gi|78114087|gb|DV532476.1|DV532476

EST:     CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAG                         AGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT
genomic: CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAGgttcgtgccc ... ttgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT

EST: gi|211472271|gb|FL205289.1|FL205289

EST:     CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAG                         AGGCGGTATGGCTGCCGGGCGATGATGCTTGAAACTGNGGGCTGCGGTGCC
genomic: CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAGgttcgtgccc ... ttgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGG-CTGCGGTGCC

EST: gi|148960977|gb|EE011674.2|EE011674

EST:     CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAG                         AGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT
genomic: CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAGgttcgtgccc ... ttgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT

EST: gi|149015792|gb|EE045489.2|EE045489

EST:     CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAG                         AGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT
genomic: CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAGgttcgtgccc ... ttgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT

EST: gi|89250644|gb|DY622430.1|DY622430

EST:     CATACTGGACCGTCCAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAG                         AGGCGGTATGGCTGCCGGGCGATGATGCTGGAAAACGTGGCTGCGGGGCCT
genomic: CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAGgttcgtgccc ... ttgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT

EST: gi|71439210|gb|DR820260.1|DR820260

EST:     CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAG                         AGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT
genomic: CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAGgttcgtgccc ... ttgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT

EST: gi|148930596|gb|EE285266.2|EE285266

EST:     CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAG                         AGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT
genomic: CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAGgttcgtgccc ... ttgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT

EST: gi|13150527|gb|BG320849.1|BG320849

EST:     CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAG                         AGGYGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT
genomic: CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAGgttcgtgccc ... ttgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT

EST: gi|148949605|gb|EC895076.2|EC895076

EST:     CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAG                         AGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT
genomic: CATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAGgttcgtgccc ... ttgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCT

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 3 RNA-Seq libraries.

Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 183

CATTGACCTCACCAGACACCATGAGCCCAAGACGCTGATGGATAAGGTCGCATACTGGACCGTCAAGTCGCTGCGCTTCCCCACGGACATCTTCTTCCAGgttcgtgccc ... ttgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCTGGGATGGTGGGCGGCATGCTGCTCCACCTGCGCTCACTCCGCCGCTTCG

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 46

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gatcattcatgtgctgttgtaagctgaccctgtgaattgggcgaattgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCTGGGATGGTGGGCGGCATGCTGCTCCACCTGCGCTCACTCCGCCGCTTCG

                     agctgac  putative branch site (score: 164)

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgtcgaaatgatctgcatattttgaaggaaggttgaaaggtcgatcattcatgtgctgttgtaagctgaccctgtgaattgggcgaattgtctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCTGGGATGGTGGGCGGCATGCTGCTCCACCTGCGCTCACTCCGCCGCTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
gcatgtc
- - - - - - - -ctgcata
- - - - - - - - - - - - - - - - - - - - - - - - -attcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaattg