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

...agcctagtttgtgcatccaatctaaaatctgtagtttggtcatataatggaatttaaaagctattcagagtatgtttgagactgacttttttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGA

Basic information

species	Zea mays
transcript	GRMZM2G078756_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 8

-agcctag-tttgtgcatccaatctaaaatctgtagtttggtcatataatggaatttaaaa-gctattcagagtatgtttgagactgac---ttttttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGA
  |||||  ||||||| || ||      ||    ||| || | ||| | |||||||||    |||  ||| | | | | | || || |    || || |||||||||||||||| ||||| |||||||||||||||||||| ||||| || ||||||||||| ||||| |||||||||||||||||||| || || || |||||||
gtgcctaactttgtgcgtctaac-----attaccagtatgatgatacactggaatttattgtgctcgtcataattt-tatcaggctaaagtgttgttcgtttgcagGTAAAACTAATTGACAATTTCACCAACAAGAAAGGAATGACGAGCCATTGCTACAGGATAGCCTATAGGTCAATGGAACGTTCACTTACCGATGAGGAGA

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 8

agcctagtttgtgcatccaatctaaaatctgtagtttggtcatataatggaatttaaaagctattcagagtatgtttgagactgacttttttgt-ttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGA
    |||||| |  ||   ||       |  |  |||       |  |  | |      | |       || |||||  |  |  ||| ||    ||||||||  || | || || || ||||||||||||||||| ||||| || || ||||| || || ||||||||||| ||||||||||| ||||| || ||||| |
catttagttttta-ataggattatttccccctttttttaatgagtgctacattaagtttgttcccttttgtctgtttttgttttgcttcttgaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGCTATAGGATTGCATATAGGTCTATGGAACGTTCTCTCACTGATGAGGAAA

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 10

------agcctagtttgtgcatccaatctaaaatctgtagtttggtcatataatggaatttaaaagctattcagagtatgtttgagactgacttttttg-tttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGA
      | |    ||    |||||  ||     | | |  |   ||  || | |  | ||| |   || ||     | |||||  |  || ||| |    |||||||||  || | || || |||||||||||||||||||| ||||| || || ||||| || || ||||||||||| ||||||||||| ||||| || ||||| |
gtttttaacaggattatgacatcctttcccccttttttcatg-agtgctacatta-agtttgatccctttt-----tctgtttttgtttggcttctcgaatttgcagGTGCAATTAATAGACAATTTCACCAACAAGAAAGGAATGACCAGCCACTGCTATAGGATTGCATATAGGTCTATGGAACGTTCACTCACTGATGAGGAAA

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv19s0027g01480.t01 (Vitis vinifera), 3'ss of exon 3

agcctagtttgtgcatccaatctaaaatctgtagtttggtcatataatggaatttaaaagctattcagagtatgtttgagac------tgacttttttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGA
     |    |||     |||   || ||  || |||  |  |    || || | ||   | |||| ||   | | |||         |   |||||   || |||||  || | || || |||||||||||||||||||| ||||| ||||| || ||  | ||||||||  |||| ||||| ||||| || ||||| |||||||
--ttgaaacagtggccataat---aagtccctattttcctagtgcc-tgaaagtgaagctccattctgaagttttctgaactataagatacatttttgacttccagGTGCAATTGATCGACAATTTCACCAACAAGAAAGGAATGACCAGTCAATGTTATCGGATAGCATACCGGTCCATGGAGCGTTCACTTACAGATGAGGAGA

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 3'ss of exon 8

agcctagtttgtgcatccaatctaaaatctgtagtttggtcatataatggaatttaaaagctattcagagtatgtttgagactg------acttttttg-tttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGA
    ||    |||     |||   || ||  || |||  |  |    || || | ||   | |||| ||   | ||  | |||       || ||||||  || |||||  || | || || |||||||||||||| ||||| ||||| ||||| || ||  | ||||||||  |||| ||||| ||||| || ||||| |||||||
--gttaaacagtggccataat---aagtccctattttcctagtgcc-tgaaagtgaagctccattctgaa-gttttctaaactataagatacatttttgacttccagGTGCAATTGATCGACAATTTCACCAACAACAAAGGAATGACCAGTCAATGTTATCGGATAGCATACCGGTCCATGGAGCGTTCACTTACAGATGAGGAGA

upper sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 8

--agcctagtttgtgcatccaatctaaaatctgtagtttggtcatataatggaatttaaaagctattcagagtatgtttgagactgacttttttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGA
       ||||     |      |      ||     |  | |  | | ||||  || |  |  |       ||   |      |   |||||   |  |||||  || | ||||| |||||||||||||||||||| ||||| ||||| || ||  | ||||||||  |||| ||||| ||||| || ||||| |||||||
gtgaaacagttgccataatggtccctgttcctcccagt--gcctgaaagtggagcttcattgtgaagttttctaaactattagatatatttttgactgccagGTGCAATTGATTGACAATTTCACCAACAAGAAAGGAATGACCAGTCAATGTTATCGGATAGCATACCGGTCCATGGAGCGTTCACTTACAGATGAGGAGA

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|32794286|gb|CD946522.1|CD946522

EST:     GATCTTGTTGAGGAG                         GTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC
genomic: GATCTTGTTGAGGAGgtatggcaac ... ttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC

EST: gi|32856608|gb|CD996289.1|CD996289

EST:     AC-ACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAG                         GTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC
genomic: ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAGgtatggcaac ... ttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC

EST: gi|211308521|gb|FL467499.1|FL467499

EST:     ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAG                         GTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC
genomic: ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAGgtatggcaac ... ttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC

EST: gi|76910024|gb|DV163657.1|DV163657

EST:     ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAG                         GTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC
genomic: ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAGgtatggcaac ... ttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC

EST: gi|31072245|gb|BQ479053.1|BQ479053

EST:     ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAG                         GTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC
genomic: ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAGgtatggcaac ... ttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC

EST: gi|71762613|gb|DR960550.1|DR960550

EST:     ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAG                         GTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC
genomic: ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAGgtatggcaac ... ttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC

EST: gi|78079223|gb|DV507635.1|DV507635

EST:     ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAG                         GTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC
genomic: ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAGgtatggcaac ... ttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC

EST: gi|60395362|gb|DN228231.1|DN228231

EST:     ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAG                         GTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC
genomic: ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAGgtatggcaac ... ttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC

EST: gi|71310636|gb|DR791614.1|DR791614

EST:     ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAG                         GTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC
genomic: ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAGgtatggcaac ... ttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC

EST: gi|211026939|gb|FL261356.1|FL261356

EST:     ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAG                         GTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC
genomic: ACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAGgtatggcaac ... ttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGC

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), 47 (downstream exon)
Score: 171

TCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTGAGGAGgtatggcaac ... ttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGA

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 217

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 119

Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 120

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aatggaatttaaaagctattcagagtatgtttgagactgacttttttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGA

                                  gactgac  putative branch site (score: 120)
                                        cttttttgttt  CT-rich tract
     aatttaaaagctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcctagtttgtgcatccaatctaaaatctgtagtttggtcatataatggaatttaaaagctattcagagtatgtttgagactgacttttttgtttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - -tgcatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtttg