ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TCCGACGCCGCCGCCACGGCGGCCGCCGAGGCCAAAGCCAAGGTGTTCCGCCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttctgtttcccacgctcccgatgctgcttgctattaggcttgagatttctagatcggatctgggtgggcctcggtgctcgggttgcgggctact...

Basic information

species	Zea mays
transcript	GRMZM2G159388_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G159388_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g12650.1 (Oryza sativa), 5'ss of exon 1

TCCGACGCCGCCGCCACGGCGGCCGCCGAGGCCAAAGCCAAGGTGTTCCGCCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttctgtttcccacgctcccgatgctgcttgctattaggcttgagatt--tctagatcggatctgggtgggcctcggtgctcgggttgcgggctact
   ||  | || ||  | || || ||||||||||| ||||||||||||||||| ||||| |||||| ||||||||||||||| ||||||||| ||||| ||||||| |    |  |   |||   |||    ||  || |  |  |  |   |  | | | | | || ||   | ||    | |   ||| || |  ||   
GTTGATTCGGCTGCTGCTGCCGCGGCCGAGGCCAAGGCCAAGGTGTTCCGCCTCTTCGGGCGCGAGGAGCCCATCCACAAGGTCCTCGGTGGAGGCAAACgtatggctgctctctctctgctgatgatctctctctctctctgtttcaaagctgatttggtttgaatttgttagagcgggtggggatgggctg-gatctgg-

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|211019782|gb|FL168529.1|FL168529

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211011437|gb|FL168488.1|FL168488

EST:     TCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211126432|gb|FL168548.1|FL168548

EST:     TCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211011439|gb|FL168490.1|FL168490

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211126436|gb|FL168552.1|FL168552

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|37377979|gb|CF625638.1|CF625638

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211017001|gb|FL168520.1|FL168520

EST:     TCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|71319886|gb|DR796701.1|DR796701

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211019791|gb|FL168538.1|FL168538

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211016995|gb|FL168514.1|FL168514

EST:     TCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|29946755|gb|CB816309.1|CB816309

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211019785|gb|FL168532.1|FL168532

EST:     TCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211011443|gb|FL168494.1|FL168494

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211017008|gb|FL168527.1|FL168527

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|76915381|gb|DV165958.1|DV165958

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|22545660|gb|BU098019.1|BU098019

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211011446|gb|FL168497.1|FL168497

EST:     TCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|60395367|gb|DN228236.1|DN228236

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211019790|gb|FL168537.1|FL168537

EST:     TCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|9952806|gb|BE639389.1|BE639389

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211126428|gb|FL168544.1|FL168544

EST:     CCTTTTCRGCCGCGAGCAGCNCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGT
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGT

EST: gi|211126427|gb|FL168543.1|FL168543

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|6564128|gb|AW231750.1|AW231750

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|30031743|gb|CB833594.1|CB833594

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211019793|gb|FL168540.1|FL168540

EST:     CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211011441|gb|FL168492.1|FL168492

EST:     CTCTTCGGCCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGGAACAAGAACATCTCTGCTGGAATACTT
genomic: CTTTTCGGCC-GCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGG-AACAAGAACATCTCTGCTGGAGTACTT

EST: gi|211014221|gb|FL168506.1|FL168506

EST:     TCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211126439|gb|FL168555.1|FL168555

EST:     TCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211014223|gb|FL168508.1|FL168508

EST:     TCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

EST: gi|211017003|gb|FL168522.1|FL168522

EST:     TCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGC                         CTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAATACTTG
genomic: CCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTG

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: 451

TCCGACGCCGCCGCCACGGCGGCCGCCGAGGCCAAAGCCAAGGTGTTCCGCCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttct ... tattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTGGTGGTGCCACAGCAATCTGGATCTTATTTGAATTGCTTGGCTACCATCT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 427

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 140

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCGACGCCGCCGCCACGGCGGCCGCCGAGGCCAAAGCCAAGGTGTTCCGCCTTTTCGGCCGCGAGCAGCCCATCCACAAGGCCCTCGGTGGCGGCAAGCgtatggttctgtttcccacgctcccgatgctgcttgctattaggcttgagatttctagatcggatctgggtgggcctcggtgctcgggttgcgggctact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccacgc