ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...gatcatatggaatgtcaaaatctaactaacttcatactttatgcaattttaagggagatagttctcaactatattgatatattatccttgacttgttcagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGATCTTCTGAAGGATAAACAAGCCCTTCAGAGGCTTACTGAGGCAGCAGAGA

Basic information

species	Zea mays
transcript	GRMZM2G001500_T02
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G001500_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g14070.1 (Oryza sativa), 3'ss of exon 3

gatcatatggaatgtcaaaatctaactaacttcatactttat--gcaat-tttaagggagatagttctcaactatattgatatattatccttgacttgttcagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGATCTTCTGAAGGATAAACAAGCCCTTCAGAGGCTTACTGAGGCAGCAGAGA
   |||    ||  |    |||     ||||   |  ||||    || | |   |     || ||| |    ||  |||| || |||||||||| || |  ||| | | || |||||||||||||||||||| |||||||||||| | |||||||||||||| || ||||||||||| ||| | || ||||||||||||||||
--ccatggacaacatacctatcagttgaactgattcttttactgacagtatgctatatttattgtttttttttaatttga-atgttatccttgaattatgtagAAAGTTGTGGATTGGCTTGCTAGCAACTTTAAGAAAGATGAAGGCATTGATCTTCTGAAAGACAAACAAGCCCTGCAGCGACTCACTGAGGCAGCAGAGA

upper sequence: GRMZM2G001500_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G00410.1 (Glycine max), 3'ss of exon 2

-gatcatatggaatgtcaaaatctaactaacttcatactttatgcaattttaagggaga-tagttctcaactatattgatatattatccttgacttgtt-cagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGATCTTCTGAAGGATAAACAAGCCCTTCAGAGGCTTACTGAGGCAGCAGAGA
  | | |      | |           |    || |   ||  | | | | |     || |  || ||   | || |     | |     |  | | ||  ||||||| || |||||||| |||  ||||||||||| ||||||| | || || ||| |||| || |||||||| |||||| | || |||||| |||| ||||
gtacctttccccttctttcttctcttgtcttgtcttgtctttagtagtgtgagtaatgaatgattttcttttttacttgctaactgcttgtttcctattatagAGAATTGTTGATTGGCTGGCTTCCAACTTCAAGAGAGATGAAGGCATAGACCTTTTGAAAGACAAACAAGCTCTTCAGCGTCTCACTGAGACAGCCGAGA

upper sequence: GRMZM2G001500_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ32911 (Selaginella moellendorffii), 3'ss of exon 4

gatcatatggaatgtcaaaatctaactaacttcatactttatgcaattttaagggagatagttctcaactatattgatatattatccttgacttgttcagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGATCTTCTGAAGGATAAACAAGCCCTTCAGAGGCTTACTGAGGCAGCAGAGA
                                         ||| |     |   |   || |||    ||| ||  ||  |  |  | | | |   |||||||| || || ||||| ||   ||||||||||||||| ||| | || |||||||| ||||| || ||||| ||||| ||||| || ||| | |||||||
----------------------------------------gtgccacgaagatcaattaagatcttt-ttattttcttaactctttttcgtcgtaaacagAGAATTGTTGACTGGCTAGCGTCCAACTTCAAGAAAGACGAAGGAATCGATCTTCTCAAGGACAAGCAAGCACTTCAAAGGCTGACAGAGACTGCAGAGA

upper sequence: GRMZM2G001500_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ15775 (Selaginella moellendorffii), 3'ss of exon 3

gatcatatggaatgtcaaaatctaactaacttcatactttatgcaattttaagggagatagttctcaactatattgatatattatccttgacttgttcagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGATCTTCTGAAGGATAAACAAGCCCTTCAGAGGCTTACTGAGGCAGCAGAGA
                                         ||| |     |  ||   || |||    ||| ||  ||  |  |  | | | |   |||||||| || || ||||| ||   ||||||||||||||| ||| | || |||||||| ||||| || ||||| ||||| ||||| || ||| | |||||||
----------------------------------------gtgccacgaagatcgattaagatcttt-ttattttcttaactctttttcgtcgtaaacagAGAATTGTTGACTGGCTAGCGTCCAACTTCAAGAAAGACGAAGGAATCGATCTTCTCAAGGACAAGCAAGCACTTCAAAGGCTGACAGAGACTGCAGAGA

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|91875430|gb|EB405387.1|EB405387

EST:     TGCTTTCCACATCTGGTGACACACACCTTGGTGGTGATGACTTCGATAAG                         AGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGAT
genomic: TGCTTTCCACATCTGGTGACACACACCTTGGTGGTGATGACTTCGATAAGgtttgacaga ... acttgttcagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGAT

EST: gi|211323721|gb|FL059667.1|FL059667

EST:     TGCTTTCCACATCTGGTGACACACACCTTGGTGGTGATGACTTCGATAAG                         AGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGAT
genomic: TGCTTTCCACATCTGGTGACACACACCTTGGTGGTGATGACTTCGATAAGgtttgacaga ... acttgttcagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGAT

EST: gi|211323718|gb|FL059664.1|FL059664

EST:     TGCTTTCCACATCTGGTGACACACACCTTGGTGGTGATGACTTCGATAAG                         AGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGAT
genomic: TGCTTTCCACATCTGGTGACACACACCTTGGTGGTGATGACTTCGATAAGgtttgacaga ... acttgttcagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGAT

EST: gi|211323720|gb|FL059666.1|FL059666

EST:     TGCTTTCCACATCTGGTGACACACACCTTGGTGGTGATGACTTCGATAAG                         AGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGAT
genomic: TGCTTTCCACATCTGGTGACACACACCTTGGTGGTGATGACTTCGATAAGgtttgacaga ... acttgttcagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGAT

EST: gi|211323719|gb|FL059665.1|FL059665

EST:     TGCTTTCCACATCTGGTGACACACACCTTGGTGGTGATGACTTCGATAAG                         AGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGAT
genomic: TGCTTTCCACATCTGGTGACACACACCTTGGTGGTGATGACTTCGATAAGgtttgacaga ... acttgttcagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGAT

EST: gi|211323722|gb|FL059668.1|FL059668

EST:     TGCTTTCCACATCTGGTGACACACACCTTGGTGGTGATGACTTCGATAAG                         AGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGAT
genomic: TGCTTTCCACATCTGGTGACACACACCTTGGTGGTGATGACTTCGATAAGgtttgacaga ... acttgttcagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGAT

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: 84

TATTGGAAGTTGGTGATGGTGTGTTTGAGGTGCTTTCCACATCTGGTGACACACACCTTGGTGGTGATGACTTCGATAAGgtttgacaga ... acttgttcagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGATCTTCTGAAGGATAAACAAGCCCTTCAGAGGCTTACTGAGGCAGCAGAGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 234

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 198

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

attttaagggagatagttctcaactatattgatatattatccttgacttgttcagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGATCTTCTGAAGGATAAACAAGCCCTTCAGAGGCTTACTGAGGCAGCAGAGA

                                              cttgttc  CT-rich tract
                   tcaactatattgatat  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatcatatggaatgtcaaaatctaactaacttcatactttatgcaattttaagggagatagttctcaactatattgatatattatccttgacttgttcagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGATCTTCTGAAGGATAAACAAGCCCTTCAGAGGCTTACTGAGGCAGCAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - ttatgca