ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCATATCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacagaacactattttcttgatttcttcagagtttatggtaacttattaaccttcaagagcaatctttgatgatgaccccttttgctgtag

Basic information

species	Zea mays
transcript	GRMZM2G086497_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G086497_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g54920.1 (Oryza sativa), 5'ss of exon 4

AACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCATATCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacagaacactattttcttgatttcttcagagtttatggtaacttattaaccttcaagagcaatctttgatgatgaccccttttgctgtag
|||||||||| || |||||||| |||| |||||| |||||||||||||||||||||||||||||||||||| |||||| |||||||||||||||||||||||| | ||    |      || |  | |  ||||| ||  ||| ||| | |   || ||  |||||| | |||||  |  |    | ||| |  ||
AACCAGCATATTATAACTATGTCTGTGCGATGTTACTACTGAATGGCATATCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacactagcc-----cttttgtagtatttcagtgtg-atgctaattca---acatttgagagcattatttgagca-aatatttcttgttacag

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|20507678|gb|BQ279726.1|BQ279726

EST:     TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT
genomic: TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT

EST: gi|149101731|gb|EE187868.2|EE187868

EST:     TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATTTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT
genomic: TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT

EST: gi|211021098|gb|FL442866.1|FL442866

EST:     TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT
genomic: TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT

EST: gi|211314374|gb|FL453743.1|FL453743

EST:     TCACTGTTTGGATGTTTCGTTATTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTTCCCCTCC
genomic: TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTT-CCCCTCC

EST: gi|28982919|gb|BQ538440.2|BQ538440

EST:     TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT
genomic: TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT

EST: gi|149004863|gb|EE039371.2|EE039371

EST:     TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATTTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT
genomic: TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT

EST: gi|113601941|gb|DW766559.1|DW766559

EST:     CTGGATTTGGTTTATG                         GTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT
genomic: CTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT

EST: gi|78123014|gb|DV541398.1|DV541398

EST:     TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT
genomic: TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT

EST: gi|6865283|gb|AW360633.1|AW360633

EST:     TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT
genomic: TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT

EST: gi|116814069|gb|EC856569.1|EC856569

EST:     TCACTGTTTGGATGTTTCGTTATTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT
genomic: TCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCT

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), 48 (downstream exon)
Score: 172

AACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCATATCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCAGACTTCTTCCAG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 148

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 245

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 163

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACCAGCATACTACAACTATGTATGTGTGATGTTGCTACTGAATGGCATATCACTGTTTGGATGTTTCCTTATTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacagaacactattttcttgatttcttcagagtttatggtaacttattaaccttcaagagcaatctttgatgatgaccccttttgctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA