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

...attcttttcctgattgaagttcgtattaataattaggtgcttcataccaatttgtacatgctaatgctaatgttttggatttgctaacgtgactgtgcagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG

Basic information

species	Zea mays
transcript	GRMZM2G010823_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 5

attcttttcctgattg--aagttcgtattaataattaggtgcttcataccaatttgtaca-tgctaatgctaatgttttggatttgctaacgtgactgtgcagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG
       | ||| |||  ||   |  |  |   || |  |||    |     ||  || |      |||||  | |     |  |   ||| ||      ||| || |||| ||| ||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||| ||||| || ||| | ||||| 
---gcacttctggttggcaacaccagaagatagatgatatgcagtgtgttccttcatatagcatctatgctgttctaacaaaagtttcaacttggtgtaacagTCTGTTGAATTTCAAGACATAATTAAAATTGGGCGTACACATACCCAAGATGCCACCCCATTGACCCTTGGCCAAGAGTTCAGCGGTTACGCCACACAA

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 5

attcttttcctgattgaagttcgtattaataattaggtgcttcataccaatttgtacatgctaatgctaatgttttggatttgctaacgtgactgtg-cagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG
|||    |    |   || ||  | | | |  ||     | |  |     ||| ||   | |     | || |||||  | | ||      | | |  ||| | ||||| || ||||| ||  | || |||||||| || ||||| |||||||| || || ||||||||||| ||||| || ||||| || |||||||| 
atttgactttgtaactaattttctttaattggttttcatcattgtttttgttt-tatcagttttaatttattttttgcctcttctttttaaaatataacagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGGCAAGAGTTTAGTGGGTATACTACACAA

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 5

attcttttcctgattgaagttcgtattaataattaggtgcttcataccaatttgtacatgctaatgctaatgttttggatttg----ctaacgtgactgtgcagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG
  |   ||  | | |||  ||| ||  |||  ||   |   |         || ||   | |  |  | |  |||| |  ||     ||||    | | | ||| |  |||| |||||||| ||  | || |||||||| || ||||| |||||||| || || ||||||||||| ||||| || ||||| || |||||||| 
--tggctttgtaactgattttcttaa-aatggttttttatctttgcttttgttttattagtttttatttaaatttttgccttttcctctaaaaaaaatat-cagTCAGTTGAATTTAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGATATACTACACAA

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 5

attcttttcctgattgaagttcgtattaataattaggtgcttcataccaatttgtacatgctaatgctaatgttttggatttgctaacgtgactgtgc-agACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG
 ||    |    ||| |  ||  | | | |  ||     | |  |     ||| ||   | |     | || |||||  | | ||      | | | | || | ||||| || ||||| ||  | || |||||||| || ||||| |||||||| || || ||||||||||| ||||| || ||||| || |||||||| 
-tttgactttgtatttagttttctttaattggtttttatcattgtttttgtttttatcagttttaatttattttttgcctcttctttttaaaatataccagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGGTATACTACACAA

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 6

attcttttcctgattgaagttcgtattaataattagg--tgcttcataccaatttgtacatgctaatgctaatgttttggatttgctaacgtgactgtg--cagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG
        |||   | |  |   || || |||| |||  | ||   |  ||   | || |    | |  |     | ||  |||||| |  |   | |   ||| |||||||||| ||||| || ||||||||||| ||||| || || |||||||| || || |||||| | |||||||| || ||||| ||   |||||| 
---ggcagcctatgtaatatatttaata-taatgaggactactaggtgacacaatataaaaatcattcttgcctctatgactttgcttattttgttttttccagTCTATTGAGTTCAAAGATATTATTAAAATTGGGCGTACTCACACTCAAGATGCAACGCCTTTGACTTTGGGCCAAGAGTTTAGTGGGTATTATACACAA

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0060g01700.t01 (Vitis vinifera), 3'ss of exon 3

attcttttcctgattgaagttcgtattaataattaggtgcttcataccaatttgtacatgc--taatg-ctaatgttttggatttgctaacgtgactgtgc-agACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG
  || |    | || | | |  || | || | |    | |||| |      ||||  || |  || ||  | |||  ||    |   || | |   | ||| || |  |||| || |||||||| ||||| |||||||| || || |||||||||||||| || || || ||||| ||||| || ||||||||  | || || 
--tcatcaaataatggcaatgtgt-tcaacactgttttacttc-tgttgtcttgtgaataccttactgatttatgcattcctgtatttatctttgttatgccagTCCCTTGAATTCAAAGACATTATTAAGATTGGACGGACCCACACCCAAGATGCCACACCTTTAACCCTTGGGCAAGAGTTTAGTGGCTATTCAACTCAA

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|148999094|gb|EE030327.2|EE030327

EST:     CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAA                         ACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGAT
genomic: CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAAgtattaactt ... gactgtgcagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGAT

EST: gi|78111379|gb|DV529776.1|DV529776

EST:     CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAA                         ACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGAT
genomic: CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAAgtattaactt ... gactgtgcagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGAT

EST: gi|149089384|gb|EE178623.2|EE178623

EST:     CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAA                         ACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGAT
genomic: CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAAgtattaactt ... gactgtgcagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGAT

EST: gi|149001505|gb|EE038811.2|EE038811

EST:     CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAA                         ACTATTGAGTTTTAAGACA
genomic: CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAAgtattaactt ... gactgtgcagACTATTGAGTTTAAAGACA

EST: gi|148951891|gb|EC897665.2|EC897665

EST:     CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAA                         ACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGAT
genomic: CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAAgtattaactt ... gactgtgcagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGAT

EST: gi|211324570|gb|FL223787.1|FL223787

EST:     CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAA                         ACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGAT
genomic: CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAAgtattaactt ... gactgtgcagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGAT

EST: gi|32797316|gb|CD949552.1|CD949552

EST:     CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAA                         ACTGTTGAGTTTA
genomic: CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAAgtattaactt ... gactgtgcagACTATTGAGTTTA

EST: gi|91877250|gb|EB407207.1|EB407207

EST:     CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAA                         ACTATTGAGTTTAAAGACATAATTA
genomic: CGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAAgtattaactt ... gactgtgcagACTATTGAGTTTAAAGACATAATTA

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: 246

GTAATGCATATAGCGACGGCCGTTGAGATACATTCGAGGTTTATCCCAAGTTTGCAACAGTTGCATGATTCACTTCATTCGAAAgtattaactt ... gactgtgcagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 276

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 501

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

accaatttgtacatgctaatgctaatgttttggatttgctaacgtgactgtgcagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG

                                    tgctaac  putative branch site (score: 501)
                      taatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcttttcctgattgaagttcgtattaataattaggtgcttcataccaatttgtacatgctaatgctaatgttttggatttgctaacgtgactgtgcagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG

- - - - -ctgattg
- - - - - - - - - - - - - - - - - - gtgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - tacatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgctaa