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

...gaagtataaaaacttgcacactcataattcctgttactgttttgaaacttgcgtcccatcttcccagtcctgacgtttacctttctttacatggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA

Basic information

species	Zea mays
transcript	GRMZM2G006790_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G006790_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g40720.1 (Oryza sativa), 3'ss of exon 4

-----------gaagtataaaaacttgcacactcataattcctgttactgttttgaaacttgcgtcccatcttcccagtcctgacgtttacctttctttacatggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA
           | | | |||||| ||  | | | | ||||||  | |  ||||   || ||  |||| | | |        | ||  ||  |||| ||| |||||||| |||||||||||||||||||||||| ||||||||||| ||||| || || |||||||| |||||||||||||| || ||||| ||||||||||| ||  ||||
atttctctatagtaatctaaaaatttctagattgacaattcccatca--gtttcagaa-ttaagtcctaacatg-------taacactt-tctttttttgcatggcaccagAGGAAATGGACTGGGACAAGAATGGAATGGTGACCTTCAAAGAATTTCTGTTTGCATTCACTCGCTGGGTTGGGATTGACGAAAATGAGGACGACAATGA

upper sequence: GRMZM2G006790_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G33830.1 (Glycine max), 3'ss of exon 5

-----gaagtataaaaacttgcacactcataattcctgttactgttttgaaacttgcgtcccatcttcccagtcctgacgtttacctttctttacatggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA
       ||||  ||  ||    ||    |  |  |||||  |  ||   |||| |  |   || | |  |||  |    ||    | ||| || |   |   ||| |||||||| ||||| || || |||||||| |  ||||||||||| || ||||| || || || ||||| ||||||||||||  ||| ||||| ||  |
tctatccagtagcaactctaaatcaactttg-tctctgttttttcttcctaactagtattttatttactaagtatt----ttgttttctctgtaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGACGATGAGGAAAA

upper sequence: GRMZM2G006790_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 5

--gaagtataaaaacttgcacactcataattcctgttactgttttgaaacttgcgtcccatcttcccagtcctgacgtttacctttctttacatggcact--agAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA
    ||||  ||  ||    ||  | |  |   ||||  |  ||   | || |  |   || | |  |         |||   ||||| | ||     ||  ||| |||||||| ||||| || || ||||||||||  ||||||||||| || ||||| || || || ||||| ||||||||||||  |||||| || ||  |
atacagtagcaactctaaatcaaccttc-tctttgttttttcttcctagctagtattttatttactaa---taagtattttgttttctctgcaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGAGGACGAGGAAAA

upper sequence: GRMZM2G006790_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G26470.1 (Arabidopsis thaliana), 3'ss of exon 4

gaagtataaaaacttgcacactcataattcctgttactgttt-tgaaacttgcgtcccatcttcccagtcctgacgtttacctttctttacatggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA
              |  |  || | | | |||    ||  || | || ||| | ||   ||     |      |  || |  ||  ||    || |   |||||||||||||||||||||||||||||||||||  ||||| ||||| || || || || || |  ||||| || || ||||| ||||| || ||||| ||
-------------gtttattcttaaactccctccctcttcttctcaagctttcttct--tcactgaaccaagaatattgattttgattcctgtgtctgcagAGGAAATGGACTGGGACAAGAACGGAATGGTGAACTTCAAAGAGTTTCTCTTCGCATTTACGCAGTGGGTTGGGATAGATGAGAATGAAGAAGAAGAAGA

upper sequence: GRMZM2G006790_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv19s0015g01200.t01 (Vitis vinifera), 3'ss of exon 4

--gaagtataaaaacttgcacactcataattcctgttactgttttgaaacttgcgtcccatcttcccagtcctgacgtttacctttctttacatggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA
    |||| |          |  | || ||| |    |      |  || ||   | ||||  |        | || ||  ||| |  ||  ||      |||||| ||||| ||||| || || ||||||||||  ||||||||||| || ||||| ||||| || ||||| || ||||| || | |||||||||||| ||
tgccagtagatggttagaagctttgatgatttcctcgaacaggctccaattt-ttttccataataatctatttcac-ttggcctcttgttttattattgcagAGGAGATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTTTTTGCTTTCACCCGTTGGGTTGGGATTGACGATATTGAGGATGAAGAAGA

upper sequence: GRMZM2G006790_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S429_31V6.1 (Physcomitrella patens), 3'ss of exon 4

--gaagtataaaaacttgca-cactcat--aattcc---tgttactgttttgaaacttgcgtcccatcttcccagtc-----ctgacg---tttacctttctttacatggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA
      |      |||| || ||  |||  |||| |       ||| | || ||||| | ||    |||| | |||      ||||||   | ||| |   |    ||      |||||||||||||||||||||  |||| ||| | ||||||||||||||  |||| || |||||   |||||||||| ||||  |  | || || |||   | 
gtccgtttctcgtactttcatcatccattgaattgcgtacaccactctattcaaactcgtgtgttctcttgcaagtgtgatactgacgaaatgtacgtgagtcgcaatctgttcagAGGAAATGGACTGGGACAAAGACGGTATGATCACATTCAAGGAGTTTTTGTTCGCTTTCACCGACTGGGTAGGACTTGAGAACGACGAAGAAGAAACAGG

upper sequence: GRMZM2G006790_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ07984 (Selaginella moellendorffii), 3'ss of exon 3

gaagtataaaaacttgcacactcataattcctgttactgttttgaaacttgcgtcccatcttcccagtcctgacgtttacctttctttacatggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA
                                || ||| |   ||||       |  |   | ||    ||  | |    |||    |||  | ||   ||||||||||| ||||||||||| || ||| | || || |||||||| |||||||| || |||   ||||| || || || ||| | || |||| ||| ||
--------------------------------gtaactctcaagaaa---aaaccagaaacttccgtaactttcttcatgcttctcgtactcgaca---gAGGAAATGGATTGGGACAAGAATGGGATGATCACGTTTAAGGAGTTTCTGTTTGCTTTTACTGATTGGGTTGGGATCGAAGAAGAAGAAGATGCAGACGA

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:     GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTG                         AGGAAATGGACTGGGGACA-GAACGGAATGGTGACATTTCA-GGAGTTCCT
genomic: GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttc ... atggcactagAGGAAATGGACTGGG-ACAAGAACGGAATGGTGACATT-CAAGGAGTTCCT

EST: gi|113675155|gb|DW829924.1|DW829924

EST:     ACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCAATGAAAAGATTTG                         AGGAAATGGACTGGGAC
genomic: ACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCA-TGAAAAGATTTGgtcagttttc ... atggcactagAGGAAATGGACTGGGAC

EST: gi|50324727|gb|CO519853.1|CO519853

EST:     GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTG                         AGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT
genomic: GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttc ... atggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT

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

EST:     GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTG                         AGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT
genomic: GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttc ... atggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT

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

EST:     GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTG                         AGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT
genomic: GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttc ... atggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT

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

EST:     GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTG                         AGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT
genomic: GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttc ... atggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT

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

EST:     TACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTG                         AGGAAATGGACTGGGAC
genomic: -ACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttc ... atggcactagAGGAAATGGACTGGGAC

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

EST:     GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTG                         AGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT
genomic: GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttc ... atggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT

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

EST:     GACCACGACAGGAGAGCGCTCTTTTGGGCCTATAGCCATGAAAAGATTTG                         AGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT
genomic: GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttc ... atggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT

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

EST:     GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTG                         AGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT
genomic: GACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttc ... atggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGT

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: 38

AATAAAGATGGGTATGTGAGCAAGGATGAGATGATCCAAGCAATAAACGAGACCACGACAGGAGAGCGCTCTTCTGGGCCTATAGCCATGAAAAGATTTGgtcagttttc ... atggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 70

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 63

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 515

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aacttgcgtcccatcttcccagtcctgacgtttacctttctttacatggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA

                      tcctgac  putative branch site (score: 515)
                                    tttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagtataaaaacttgcacactcataattcctgttactgttttgaaacttgcgtcccatcttcccagtcctgacgtttacctttctttacatggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - -ataaaaa
- - - - - - cttgcac
- - - - - - - - - - - - - - - -tgttact
- - - - - - - - - - - - - - - - - - - - - - - - -tgcgtcc