ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TCAAGCCGCTCATCGACCCGCTCTGCTGCCCCAAGGGCCATACCTTCTGCAAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagcaacactgcacggtctactaatctaaattattgattgcttattagtatttttatattgatttaagtggtagttggttgggccattggggtag...

Basic information

species	Zea mays
transcript	GRMZM2G171232_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G171232_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g17170.1 (Oryza sativa), 5'ss of exon 1

TCAAGCCGCTCATCGACCCGCTCTGCTGCCCCAAGGGCCATACCTTCTGCAAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagcaacactgcacggtctactaatc---taaattattgattgcttattagtatttttatattgatttaagtggtagttggttgggccattgg-ggtag
|||||||||||||| ||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||       |  |    | ||| |  |||     | || ||  |  | ||| |  ||  |||     | ||||  ||   |    ||| |   |||| |||  
TCAAGCCGCTCATCCACCCGCTCTGCTGCCCCAAGGGCCACACCTTCTGCAAGGAGTGCATCCTCGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtacccccagattcgatcccgtccatcaattggtcatatcatgaacggtttaatcttagatttgggcag-tttagctgtcgg--aattgtgaagttggtggtt-

upper sequence: GRMZM2G171232_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ26226 (Selaginella moellendorffii), 5'ss of exon 1

TCAAGCCGCTCATCGACCCGCTCTGCTGCCCCAAGGGCCATACCTTCTGCAAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagcaacactgcacggtctactaatctaaattattgattgcttattagtatttttatattgatttaagtggtagttggttgggccattggggtag
| ||||  |||| ||| ||||  |||||||  |||||||||  |||||||||||||||||| || |||| ||| || || |||||||||||||||||| |||| |      |  ||    |  | ||     |||  || |||   ||   |     ||| |      |  ||                           
TTAAGCGCCTCACCGATCCGCAGTGCTGCCAAAAGGGCCATCTCTTCTGCAAGGAGTGCATTCTCGAGTCCCTGCTAGCTCAGAAGAAGGACATCAAGAGgtatgggttttccttgatttg--tgcttggggaaaggatagat---tttgcaacgcctttgtgggcgctatag---------------------------

upper sequence: GRMZM2G171232_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ14524 (Selaginella moellendorffii), 5'ss of exon 1

TCAAGCCGCTCATCGACCCGCTCTGCTGCCCCAAGGGCCATACCTTCTGCAAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagcaacactgcacggtctactaatctaaattattgattgcttattagtatttttatattgatttaagtggtagttggttgggccattggggtag
| ||||  |||| ||| ||||  |||||||  |||||||||  |||||||||||||||||| || |||| ||| || || |||||||||||||||||| |||| | |    |  ||    |  | ||     |||  || |||   ||   |     ||| |      |  ||                           
TTAAGCGCCTCACCGATCCGCAGTGCTGCCAAAAGGGCCATCTCTTCTGCAAGGAGTGCATTCTCGAGTCCCTGCTAGCTCAGAAGAAGGACATCAAGAGgtatggattttccttgatttg--tgcttggggaaaggatagat---tttgcaacgcctttgtgggcgctacag---------------------------

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|18053180|gb|BM318838.1|BM318838

EST:     AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCG                         TAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA
genomic: AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA

EST: gi|78077082|gb|DV505516.1|DV505516

EST:     AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCG                         TAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA
genomic: AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA

EST: gi|87152189|gb|DY396978.1|DY396978

EST:     AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCG                         TAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA
genomic: AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA

EST: gi|71445351|gb|DR826401.1|DR826401

EST:     AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCG                         TAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA
genomic: AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA

EST: gi|211284703|gb|FL080850.1|FL080850

EST:     AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCG                         TAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAAGAGGA
genomic: AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA

EST: gi|211282906|gb|FL080847.1|FL080847

EST:     AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCG                         TAASSTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA
genomic: AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA

EST: gi|211284705|gb|FL080852.1|FL080852

EST:     AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCG                         TAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA
genomic: AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA

EST: gi|78077081|gb|DV505515.1|DV505515

EST:     GAAGGACATCAAGCG                         TAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA
genomic: GAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA

EST: gi|211284704|gb|FL080851.1|FL080851

EST:     AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCG                         TAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA
genomic: AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA

EST: gi|18383977|gb|BM417177.1|BM417177

EST:     AAGGAGTGCATCCTTGAGGGCCTCCTCGCCCAGAAGAAGGACATCAAGCG                         TAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA
genomic: AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA

EST: gi|50337108|gb|CO532234.1|CO532234

EST:     AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCG                         TAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA
genomic: AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA

EST: gi|19821811|gb|BQ047835.1|BQ047835

EST:     AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCG                         TAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA
genomic: AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA

EST: gi|22489123|gb|BU049046.1|BU049046

EST:     AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCG                         TAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA
genomic: AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA

EST: gi|78118289|gb|DV536675.1|DV536675

EST:     AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCG                         TAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA
genomic: AAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGA

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: 46 (upstream exon), 47 (downstream exon)
Score: 48

TCAAGCCGCTCATCGACCCGCTCTGCTGCCCCAAGGGCCATACCTTCTGCAAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagca ... attcttccagTAAGCTAGCAGCTCACGAGGCCCAGAAGAAGCAAGAGAAGGAAGAGGAGGAGGAAAAGCTAATTCTGCAGAAGGCTAAGGAGTTGGATGCCTTTGATCAG

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 106

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 79

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

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAGCCGCTCATCGACCCGCTCTGCTGCCCCAAGGGCCATACCTTCTGCAAGGAGTGCATCCTTGAGTGCCTCCTCGCCCAGAAGAAGGACATCAAGCGgtaggtagcaacactgcacggtctactaatctaaattattgattgcttattagtatttttatattgatttaagtggtagttggttgggccattggggtag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG