ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgatacgaatgtcatcgcagattaacttgaacggagacaactttgtcaacaaattttttctaattatgtattttgtactctcatttttatcag

Basic information

species	Zea mays
transcript	GRMZM2G114126_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 5

ATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgatacgaatgtcatcgcagattaacttgaacggagacaactt-tgtcaacaaat-------tttttctaattatgtattttgtactctcatt--tttatcag-------------
 ||||| || || ||||| || ||||||||||| ||||| |||||||| ||||| || |||||||||||||||||||| ||  ||||| |||| ||||||||  ||||||  |    ||| |||||  ||| |    | | ||| ||| || || | |||        ||    | || | || |   | |  ||  |  ||| |||              
CTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTATTTCATTTATTGCTGAGCAGgttagtgatatca---ccattgcaga--aaccttc-tgcaaacatcttctgccagccaatgatgctggttccacagttctttactgcatgccatcgataatttttcattttattttctcag

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G39880.1 (Glycine max), 5'ss of exon 5

-ATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgatacgaatgtcatcgcagattaacttgaacggagacaactttgtcaacaaattttttctaattatgtattttgtactctcatttttatcag----
  ||||  || ||||| || ||||||||||| || ||||| || ||||| |||||||| || |||||||||||    ||||| |||||| |  | ||||||||  ||  ||||  |    | || | |||  || |||  |  |||     |   ||  ||| || |   | | |  ||| |  |       |     |    
TCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCATTACATTTATATCAGAGCAggtgagt--tacgtttaaggt-gctgtttatttttaacaaaatcaagaaaattcccatgtttcttatgccttttttattttttttgggggggtgggagggtgc

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA11G14770.1 (Glycine max), 5'ss of exon 5

ATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgatacgaatgtcat-cgcagattaacttgaacggagacaactttg--tcaacaaattttttctaattatgtattttgtactctcatttttatcag
 ||||| ||||| || || || ||||||||||||||||| ||||||||||||||||| || |||||||||||    || || ||||||||||| || |||||   |  |  | |||| || | ||    ||||     |   |  | ||    |||     | |  |||   | | | |    || |||  | | | |   
GTACTTTGCGTACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAATTACATTTCTTGCTGAACAGgtatcttttcagtatgtgattctcatggaaactctctggtgcatgatttctactcactttctctcctctgcgtgtctttgaaatattctgttctctcttg-

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA12G06690.1 (Glycine max), 5'ss of exon 5

ATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgatacgaatgtcat-cgcagattaacttgaacggagacaactttgtcaacaaattttt-tctaattatgtat---tttgtactctcatttttatcag
 ||||| || || || || || ||||||||||||||||| ||||||||||||||||| || |||||||||||    || || ||||||||||| || |||||   |  |  | |||| || | ||    ||||     |   |  | ||| |  || | ||| | ||    | || ||   |||| | | |  | ||  |   
GTACTTTGCATACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAATTACATTTCTTGCTGAACAGgtatcttttcagtatgtgattctcatggaaactctctggtgcaggattttctacactactttctctccttctctgcatgtctttgaaatattgtgttctt---

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA15G04210.1 (Glycine max), 5'ss of exon 5

ATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgatacgaatgtcat-cgcagattaacttga--acggagacaactttgtcaacaaattttttctaattatgtattttgtactctcatttttatcag--
 |||||||| || || || || |||||||||||||| || ||||||||||||||||| ||||||| ||||||    || || ||||||||||| || |||||   |  || | |||| || | ||    ||||     ||     | ||  | |  |||   | ||||    | |||| ||| | |   |||||  |  |   
GTACTTCGCATACCAACGAACCTGGAAGCCTTTTAACCCTATCCTTGGAGAGACTTATGAGATGGCTAACCATGGTGGAATTACATTTCTTGCAGAACAGgtaccttttaagtatgtgattctcatgagaactctctcactctccccacactttttacaccatgtttcc---tttgtaatttatgccggcatttggaagaact

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|91055718|gb|EB166136.1|EB166136

EST:     AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT
genomic: AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT

EST: gi|67040089|gb|CO466344.1|CO466344

EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCCGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT
genomic: AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT

EST: gi|74236529|gb|DT644443.1|DT644443

EST:     GACTTACGAGATGGTTAACCACCAGGGCATCACATTTTCTTGCCGAGCAG                         GTAAGCCATCATCCCCCAAT
genomic: GACTTACGAGATGGTTAACCACCAGGGCATCACATTT-CTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCCCAAT

EST: gi|211354686|gb|FL118765.1|FL118765

EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCCGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGCTGC
genomic: AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGC

EST: gi|148961873|gb|EE012659.2|EE012659

EST:     AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT
genomic: AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT

EST: gi|78120437|gb|DV538821.1|DV538821

EST:     AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT
genomic: AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT

EST: gi|8367795|gb|BE050740.1|BE050740

EST:     ATTTCTTGCCGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT
genomic: ATTTCTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTT

EST: gi|87155561|gb|DY400350.1|DY400350

EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCCGAGCAG                         GTAAGCCATCATCCCC
genomic: AGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCC

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: 91

ATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgata ... tttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCAT

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 129

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 230

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 85

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCATCACATTTCTTGCCGAGCAGgtcggtgatacgaatgtcatcgcagattaacttgaacggagacaactttgtcaacaaattttttctaattatgtattttgtactctcatttttatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG