ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CCCGTCCGAGATCCTCAAGGAGTTCCTCTTCCTCGGCAGCTACGACAACGCCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttatttacatccgcacttatcattacgtgcatggatgggtagaagcatttctcagtgatacacagtgcaatatggtcagaggtgttgcataata...

Basic information

species	Zea mays
transcript	GRMZM2G174170_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G174170_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g20340.1 (Oryza sativa), 5'ss of exon 1

CCCGTCCGAGATCCTCAAGGAGTTCCTCTTCCTCGGCAGCTACGACAACGCCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttatttacatccgcact--tatcattacgtg-catggatgggtagaagcatttctcagtgatacacagtgcaatatggtcagaggtgttgcataata
|||||| |||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||| |||| ||||||||||||||| ||    |    |    | |  | | ||  | || | |    |  | |  |  ||  | || | |      |||     ||   | | ||  || |    
CCCGTCGGAGATCCTCAAGGACTTCCTCTTCCTCGGCAGCTACGACAACGCCTCCCGCTCCGAGCTGCTCAAGACCATCGGCATCTCCCACATCCTCAATgtacgccgcctcgtcttgcgattgctttgatctcttggcgtcttcgcatggtcgatttggttagggttcgttgatgcgcggggggacgggctg--gcttggc-

upper sequence: GRMZM2G174170_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv12s0059g01650.t01 (Vitis vinifera), 5'ss of exon 1

CCCGTCCGAGATCCTCAAGGAGTTCCTCTTCCTCGGCAGCTACGACAACGCCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttatttacatcc--gcacttatcattacgtgcatggatgggtagaag--catttctcagtgatacacagtgcaatatggtcagaggtgttgcataata-----
 ||||| ||||||||   |||||| || |   | ||||||||||| ||||| || ||||||||||| ||||||||    ||  |||| | | | ||||||||  |  ||   | ||    | |  | | ||| | || ||   | | ||   |  ||    |||||||| |||         | ||||   ||| ||||  |||     
TCCGTCAGAGATCCTGCCGGAGTTTCTGTATTTGGGCAGCTACGATAACGCATCGCGCTCGGAGCTTCTCAAGACTCAGGGAATCTCTCGCGTTCTCAATgtgaggatacacatattttggtatctttgatttc-tgtatatttagttaatggttcaaacttcagtgat-cacga------gtagtcatctgtgctgca-gatagggac

upper sequence: GRMZM2G174170_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ30059 (Selaginella moellendorffii), 5'ss of exon 1

---CCCGTCCGAGATCCTCAAGGAGTTCCTCTTCCTCGGCAGCTACGACAACGCCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttatttacatccgcacttatcattacgtgcatggatgggtagaagcatttctcagtgatacacagtgcaatatggtcagaggtgttgcataata
   | || | |||||  |   |   ||||| || ||||||||||||||||| |||||| |  |||||||||||||| |    ||  |  |||||||| | |||||| | |   |    ||| | |||   |     | |    |  |   |  |  | ||| ||                                       
CTTCTCGGCGGAGATTTT---GCCTTTCCTGTTTCTCGGCAGCTACGACAATGCCTCCAGGGCGGAGCTCCTCAAGGCGCAGGGAATTACGCACATCTTGAATgtaagatctctcctctcctc-ctttctagggtatcctcatactg--tggtgtttgtcttag---------------------------------------

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|91055824|gb|EB166242.1|EB166242

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

EST: gi|211352916|gb|FL033077.1|FL033077

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

EST: gi|71299488|gb|DR785755.1|DR785755

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

EST: gi|211352911|gb|FL033072.1|FL033072

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

EST: gi|91875180|gb|EB405137.1|EB405137

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

EST: gi|149112681|gb|EE295513.2|EE295513

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

EST: gi|211350512|gb|FL033069.1|FL033069

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

EST: gi|71314755|gb|DR794000.1|DR794000

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

EST: gi|78111707|gb|DV530104.1|DV530104

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

EST: gi|211350508|gb|FL033065.1|FL033065

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

EST: gi|78107086|gb|DV525504.1|DV525504

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

EST: gi|71301897|gb|DR787018.1|DR787018

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

EST: gi|211352915|gb|FL033076.1|FL033076

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

EST: gi|211350511|gb|FL033068.1|FL033068

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

EST: gi|211350510|gb|FL033067.1|FL033067

EST:     CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAAT                         ACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC
genomic: CCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGC

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: 48 (upstream exon), 49 (downstream exon)
Score: 86

CCCGTCCGAGATCCTCAAGGAGTTCCTCTTCCTCGGCAGCTACGACAACGCCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttat ... ttaattgcagACTGTACCTTTGTGCCAAAACCTTTACCGGAATTCATTCACTTATCACTGCCTTCAAGAGGACAAGACTCTGCAGTTTGATGATGCAAACCAGTTTCTAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 120

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 150

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCGTCCGAGATCCTCAAGGAGTTCCTCTTCCTCGGCAGCTACGACAACGCCTCCCGCTCGGAGCTCCTCAAGACCATCGGCGTCTCGCACATCCTCAATgtatgcttatttacatccgcacttatcattacgtgcatggatgggtagaagcatttctcagtgatacacagtgcaatatggtcagaggtgttgcataata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC