ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TCTTGAGCAAGCCATCTTTGACCGGAATACCATTACTAGTAATTGGCAACAAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcatactaagctactacactccattataatttaggtgccgtttggttcacaaaatataacgtgattcacactcgattaccagtggtaacaagtt...

Basic information

species	Zea mays
transcript	GRMZM2G007188_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G007188_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g10370.1 (Oryza sativa), 5'ss of exon 4

TCTTGAGCAAGCCATCTTTGACCGGAATACCATTACTAGTAATTGGCAACAAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcatactaagctactacactccattataatttaggtgccgtttggttcacaaaatataacgtgattcacactcgattaccagtggtaacaagtt
|  |||||||||| |||||||| || || ||||||||||| |||||||| ||||||||||| ||||||||||||||||| |||| |||||||||  |||||||||| ||  |||||||| ||||  ||  ||   |||        | |    ||||||       ||| |  |||     |||   |||  |       
TTCTGAGCAAGCCTTCTTTGACTGGGATCCCATTACTAGTCATTGGCAATAAAATTGACAAACCTGAAGCTTTCCCTAAGCAAAGCTTCACAGACGTAATgtaagtacacgctaagctattacagaccgataaggttt--------tcttacgcacaaacc----tgtgttcgaca---agttatatgtgacattgcag-

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|85152993|gb|DW587928.1|DW587928

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|71306605|gb|DR789463.1|DR789463

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|12972938|gb|BG268231.1|BG268231

EST:     AAAATTGACAAGCATGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|37382833|gb|CF628382.1|CF628382

EST:     AAAATTGACAAGCATGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|13178422|gb|BG349680.1|BG349680

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|76012951|gb|DT940121.1|DT940121

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|67012163|gb|CO440912.1|CO440912

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|13178421|gb|BG349679.1|BG349679

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|13178595|gb|BG349853.1|BG349853

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|71306606|gb|DR789464.1|DR789464

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|148969393|gb|EE020185.2|EE020185

EST:     AAATTGACAAGCC-GAAGGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAATTGACAAGCCTGAA-GCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|161586204|gb|EY952616.1|EY952616

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGG

EST: gi|76012952|gb|DT940122.1|DT940122

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|37421680|gb|CF648541.1|CF648541

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|13178420|gb|BG349678.1|BG349678

EST:     AAGATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AA-ATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|71332505|gb|DR803215.1|DR803215

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|12972958|gb|BG268241.1|BG268241

EST:     AAAATTGACAAGCATGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCCAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|71775459|gb|DR973337.1|DR973337

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|148969394|gb|EE020186.2|EE020186

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|83278732|gb|DV942740.1|DV942740

EST:     AAAATTGACAAGCATGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|6539060|gb|AW225199.1|AW225199

EST:     AAAATTGACAAGCATGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|16377996|gb|BI992228.1|BI992228

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

EST: gi|211473094|gb|FL459189.1|FL459189

EST:     AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAAT                         GGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG
genomic: AAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATG

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: 207

TCTTGAGCAAGCCATCTTTGACCGGAATACCATTACTAGTAATTGGCAACAAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcat ... gttattgcagGGGCCTAAAGACGATCACTGACCGAGAAGTGGCATGCTTCATGACATCATGCAAGAACTCGACCAACATTGATTCTGTCATTGACTGGCTGGTGAAGAAC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 89

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 102

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTGAGCAAGCCATCTTTGACCGGAATACCATTACTAGTAATTGGCAACAAAATTGACAAGCCTGAAGCTTTCCCTAAACAAACCTTCACAGAAATAATgtaagtgcatactaagctactacactccattataatttaggtgccgtttggttcacaaaatataacgtgattcacactcgattaccagtggtaacaagtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaaata