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

...gtgaatctaactttagcagcaatctacaagcggttgtgtattttttttgcattcttatcatgaatttcttttcttgcttctaatcatgtgatactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACTGGGGAATCATATGCTGGGCATTACATTTCCTGCCTTTGCAAGTCGTGTG

Basic information

species	Zea mays
transcript	GRMZM2G018950_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G018950_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g29620.1 (Oryza sativa), 3'ss of exon 3

gtgaatctaactttagcagcaatctac-aagcggttgtgtattttttttgcattcttatcatgaatttcttttctt--gcttctaatcatgtgatactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACTGGGGAATCATATGCTGGGCATTACATTTCCTGCCTTTGCAAGTCGTGTG-
  ||  | ||||  |  ||||||  || |   ||     |   |||||    |   | |||| || |    | |||   ||| |  |    | ||  || |||||||| ||  |||||||||| || | |||||||||||||||||  || ||||||||||| |||||||| || || ||| ||||||||||||||||| ||| 
--gaggcaaactaca-tagcaatgaactatatggaaaactgcctttttaatttctctttcataaagtaagctccttaaacttttctttccatcatgttgacagGCCTTCTTCACTGAGCACCCGAATTTTGCTAAAAATGATTTCTATATTACTGGGGAATCGTATGCTGGACACTATATT-CCTGCCTTTGCAAGTCGAGTGT

upper sequence: GRMZM2G018950_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0061g00530.t01 (Vitis vinifera), 3'ss of exon 3

------gtgaatctaactttagcagcaatctac---aagcggttgtg----tattttttttgcattctta---tcatgaatttcttttcttgct-----tctaat----catgtg-atactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACTGGGGAATCATATGCTGGGCATTACATTTCCTGCCTTTGCAAGTCGTGTG-
       ||  ||| || | |   |  |  |     |  |  || ||    | || |  | | |||  |    |   ||| ||  ||||||| |     | |||     | |||   |  ||  |||| |||||     |||| ||  |||  |     ||||| || ||||||||||||||||| ||||| ||||| |||||| ||||| |||||   ||| ||  
gtttctctgcttctgacctaaatggagaattgttgaagccacttatgattatgttgtcatagaattactgattttgagaaatttgtttcttgttagtactttaacattccctgtatgttatgttagGCATTTTTCAAAAAGCATCCTGAGTTCGTGCGGAATGACTTTTTCATAACTGGGGAATCGTATGCCGGGCACTACATT-CCTGCGTTTGCTGCTCGGGTTC

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|148944673|gb|EC889809.2|EC889809

EST:     CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAG                         GCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAAT
genomic: CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAGgtaatgttta ... atactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAAT

EST: gi|148944669|gb|EC889804.2|EC889804

EST:     CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAG                         GCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT
genomic: CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAGgtaatgttta ... atactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT

EST: gi|149099579|gb|EE185618.2|EE185618

EST:     CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAG                         GCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT
genomic: CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAGgtaatgttta ... atactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT

EST: gi|148969832|gb|EE020724.2|EE020724

EST:     CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAG                         GCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT
genomic: CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAGgtaatgttta ... atactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT

EST: gi|148941808|gb|EC886775.2|EC886775

EST:     CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAG                         GCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT
genomic: CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAGgtaatgttta ... atactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT

EST: gi|148962748|gb|EE013659.2|EE013659

EST:     CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAG                         GCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT
genomic: CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAGgtaatgttta ... atactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT

EST: gi|149005158|gb|EE039693.2|EE039693

EST:     TCGCCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAG                         GCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT
genomic: TCGCC-ACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAGgtaatgttta ... atactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT

EST: gi|149078258|gb|EE167015.2|EE167015

EST:     CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAG                         GCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT
genomic: CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAGgtaatgttta ... atactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT

EST: gi|149110190|gb|EE294008.2|EE294008

EST:     CTCGCCACACCGAAGCTACTATTAGCCATGATCTATATGATTTCCTGCCG                         GCCTTTTTTGCTGAGCACCCAA-GTATGCTAAAAATG
genomic: CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAGgtaatgttta ... atactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATG

EST: gi|213187795|gb|FM187023.1|FM187023

EST:     CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGACTTCCTGCAG                         GCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT
genomic: CTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAGgtaatgttta ... atactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACT

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: 292

CGACCAGCCCACTGGAACTGGGTTTAGTTACAGCTCGGATTCGCGTGACACTCGCCACAACGAAGCTACTATTAGCAATGATCTATATGATTTCCTGCAGgtaatgttta ... atactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACTGGGGAATCATATGCTGGGCATTACATTTCCTGCCTTTGCAAGTCGTGTG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 308

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 314

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 332

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttgcattcttatcatgaatttcttttcttgcttctaatcatgtgatactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACTGGGGAATCATATGCTGGGCATTACATTTCCTGCCTTTGCAAGTCGTGTG

                                ttctaat  putative branch site (score: 332)
                 aatttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatctaactttagcagcaatctacaagcggttgtgtattttttttgcattcttatcatgaatttcttttcttgcttctaatcatgtgatactgccagGCCTTTTTTGCTGAGCACCCAAAGTATGCTAAAAATGATTTCTTCATAACTGGGGAATCATATGCTGGGCATTACATTTCCTGCCTTTGCAAGTCGTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
gtgaatc
- - - - - - - -gcagcaa
- - - - - - - - - - - - - - -gcggttg
- - - - - - - - - - - - - - - - - - tgtattt
- - - - - - - - - - - - - - - - - - - - - - - -tgcattc