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

...ccataagacatagctcaatgaaattcgaggttcttttctgtctacatctacgttaacttgttaagtaatttatttgttgatgagttgagtccatttgtagGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTT

Basic information

species	Zea mays
transcript	AC235535.1_FGT001
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 3

ccata-agacatagctcaatgaaattcga--ggttcttttctgtctacatctacgttaacttgttaagtaatttatttgttgatgagttgagtccatttgtagGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTT
| ||  |     ||    || | ||   |  | || |        |    ||   ||    ||||   | ||||  ||||  |  | | |     |  ||||||||||||||||| ||||||||||| ||||| |||||||||||||||||||| ||||| || |||||||||||||||||| ||||||||||||| ||  ||
ctatttatgtgcagggtcataatatgtaattgattttaggaatcttgtgcctcttttttgatgttccatgatttgattgtctaacattggta---aactgtagGGGACGCCATGCCTCAAAGATGACAGAAGAGGAGGAAGATGAAGAATACCTTAAAGAAGAGGAAGATGCCCTTGCTGGTTCAGGGGGAACACGCTTGCTT

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 3

ccataagacatagctcaatgaaattcgaggttcttttctgtc-tacatctacgttaacttgttaagtaatttatttgttga--tgagttgagtccatttgtagGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTT
     |   ||   || | |  ||       |  ||  |||  ||||| |   ||   |  | |      || |||||| |  | |  ||       |  ||||||||| ||||||||||||||||| || || || |||||||| || || ||||| ||||| ||||||||||||| ||||||||| || || ||| | |||
---agatctatttatccagggcatctatctcttcttgttgtggtacatatttctttgttcttcataggtcttctttgtttagctaatgtggtaaggatcttagGGGACGTCATGCATCAAAGATGACAGAGGAGGAAGAAGATGAGGAGTATCTCAAGGAGGAGGAAGATGCCCTTGATGGTGCAGGAGGGACCCGTCTGGTT

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 3

-----ccataagacatagctcaatgaaattcgaggttcttttctgtctacatctacgttaacttg--ttaagtaatttatttgttgatgagttgagtccatttgt--agGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGG---GGGAACACGTTTAGTT
     |  | || |  |  |||    |   | |           | | |||   || ||    ||  | ||| || ||||    | |    ||  ||  ||   |  ||||| ||||||||||| ||  | || || ||||| ||||||||||||||||| ||||  ||||||||||  || ||     || |   ||  ||||    |   
tggttctctgagtctgatttcagaagagcactaaa-------gagacaacactgactttttgctgcataaaggaacttatcc--taacattttatgtttatgcattaagGGGTCGCCATGCATCCAATTTCACCGAGGAAGAAGAAGATGAAGAATACCTAAAAGGAGAAGAAGATGGTCTAGCAAACACACGTCTGGTGACACAACCA---

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 3

-----ccataagacatagctcaatgaaattcgaggttcttttctgtctacatctacgttaacttg--ttaagtaatttatttgttgatgagttgagtccatttgt--agGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGG---GGGAACACGTTTAGTT
     | |  || |  |  |||    ||  | |           | | |||   || ||    ||  | ||| || ||||    | |    ||  ||   | | |  ||||| ||||||||||| ||  | ||||| ||||| ||||||||||||||||| ||||  ||||||||||  || ||     || |   ||  ||||    |   
gttctctacgagtctgatttcagaagaacactaaa-------gagacgacactgactttttgctgcataaaggaacttatcc--taacattttatgtttgtgtattaagGGGTCGCCATGCATCCAATTTCACTGAGGAAGAAGAAGATGAAGAATACCTAAAAGGAGAAGAAGATGGTCTAGCAAACACACGTCTGGTGACACAACCA---

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 3

ccataagacatagctcaatgaa--attcgag-gttcttttctgtct-acatctacgttaacttgttaagtaatttatttgttgatgagttga-gtccatttgtagGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTT-
      | ||  | ||||  ||  |||  || ||| |  ||  ||| | |   || ||      || |  ||   |  |     | | |    ||| |||| |||||| ||||||||||||||  | ||||||||||||||||||||||||||||| |||| ||||||||||| | | ||   | || |          | |    
----ttggcaaggttcaaacaagcattaaagagttgtgatcaatctgatactgaccttgtgcattttaaaaaaacacattgcattaaatcactgtctattt-tagGGGTCGCCATGCATCAAAAGTAACTGAAGAAGAGGAAGATGAAGAATACCTTAAAGGGGAAGAAGATGGCTTAGCAAATACACGACTGGTG-ACTCAACCA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 3

ccataagacatagctcaatgaa---attcgaggttcttttctgtct-acatctacgttaac--ttgttaagtaatttatttgttgatgagttgagtccatttgtagGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTT-
      | ||  | ||||  ||   ||     ||| |  |   ||| | ||  || ||     || | || ||| | ||    |  | | |     ||  || ||| || ||||||||||||||  | ||||||||||||||||||||||||||||| |||| ||||||||||| | | ||   | || ||         | |    
----ttggcaaggttcaagcaatcaataaagagttgtgattaatctgatattgaccttgtgcattttaaaataactcatcgcat--taaatcaccacctattttagAGGTCGCCATGCATCAAAAGTAACTGAAGAAGAGGAAGATGAAGAATACCTTAAAGGGGAAGAAGATGGCTTAGCAAATACACGGTTGGTG-ACTCAACCA

upper sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 3

ccataagacatagctcaatgaaattcgaggttcttttc---tgtctacatctacgttaacttgttaagtaatttatttgttgatgagttgagtccatt--tgtagGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTT
   |||| | | | | ||  | ||  |  |||   |     | |  |  ||||| ||   ||  | |    ||| |       |      | ||  ||  | |||||| ||||||||||||||  |||||||||| || ||||||||||| | ||| ||||||||||||||||   |  ||||  ||||    || ||  | || 
---taagcc-tggataaac-acataggtagtttggtaaaaatattcaattctaccttggtttaatgatggctttctcctcctttattcccaatcacttaatttagGGGTCGCCATGCATCAAAAGTGACTGAAGAGGAAGAAGATGAAGAGTGCCTGAAAGAGGAAGAAGATGGTTTATCTGGGACAGGAAACACGCGGCTGGTG

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|211342489|gb|FL449460.1|FL449460

EST:     GCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCGGGAG                         GGGACGCCATGCATCAAAGATGACT-AAGAAGAGG
genomic: GCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCGGGAGgtaacattgg ... ccatttgtagGGGACGCCATGCATCAAAGATGACTGAAGAAGAGG

EST: gi|149075149|gb|EE163643.2|EE163643

EST:     GCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCGGGAG                         GGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCT
genomic: GCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCGGGAGgtaacattgg ... ccatttgtagGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCT

EST: gi|22491353|gb|BU051276.1|BU051276

EST:     GCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCGGGAG                         GGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCT
genomic: GCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCGGGAGgtaacattgg ... ccatttgtagGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCT

EST: gi|19351041|gb|BM895573.1|BM895573

EST:     GCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCGGGAG                         GGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCT
genomic: GCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCGGGAGgtaacattgg ... ccatttgtagGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCT

EST: gi|87153564|gb|DY398353.1|DY398353

EST:     GCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCGGGAG                         GGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCT
genomic: GCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCGGGAGgtaacattgg ... ccatttgtagGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCT

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: 364

ATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATATTTGCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCGGGAGgtaacattgg ... ccatttgtagGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 162

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atctacgttaacttgttaagtaatttatttgttgatgagttgagtccatttgtagGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTT

                                            tccattt  CT-rich tract
       ttaacttgttaagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccataagacatagctcaatgaaattcgaggttcttttctgtctacatctacgttaacttgttaagtaatttatttgttgatgagttgagtccatttgtagGGGACGCCATGCATCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - -caatgaaa
- - - - - - - - - - - - - - - - -ttttctg
- - - - - - - - - - - - - - - - - - - - -ctacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgatg