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

...catgacccactcatgtaggagcatttggcactgtgtctgtcctttttcttacacctgtaaatagacattgatgacaaggtttttgtgttgtgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGGATTCGATCTCTGCTCCCCCAGCTTTTGCAGGAGAGTTCCCATCTAACCA

Basic information

species	Zea mays
transcript	GRMZM2G125777_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G125777_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g44820.1 (Oryza sativa), 3'ss of exon 4

-catgacccactcatgtaggagcatttggcactgtgtctgtcctttttcttacacctgtaaatagacattgatgacaaggtttttgtgttgtgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGGATTCGATCTCTGCTCCCCCAGCTTTTGCAGGAG---AGTTCCCATCTAACCA
   ||   ||| ||  | | |     |  | |  || ||| || ||  |||  |||||||| |  |||||  ||||||| | |||||  | | ||| ||||||   ||| | |||||||||   || || ||| | ||||||| |||  ||||||| |||||||||||||| |||||||||| ||   |||||||| |||    
cagtgttacacacaattggcatgtgatttctcattgcctggccattaacttgtacctgtaattgaacattattgacaag-tgtttgtactatattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGGATTCAATCTCTGCTCCCCCTGCTTTTGCAGCAGCAGAGTTCCCAGCTAG---

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|78079887|gb|DV508299.1|DV508299

EST:     TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAG                         ATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG
genomic: TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAGgtaatcttat ... tgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG

EST: gi|110540958|gb|EE044878.1|EE044878

EST:     TAGTCAGTTAAATTGTGTTGTTTTACCAG                         ATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG
genomic: TAGTCAGTTAAATTGTGTTGTTTTACCAGgtaatcttat ... tgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG

EST: gi|211005049|gb|FL466904.1|FL466904

EST:     TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAG                         ATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG
genomic: TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAGgtaatcttat ... tgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG

EST: gi|211005050|gb|FL466905.1|FL466905

EST:     TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAG                         ATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG
genomic: TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAGgtaatcttat ... tgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG

EST: gi|149043144|gb|EE047289.2|EE047289

EST:     TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAG                         ATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG
genomic: TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAGgtaatcttat ... tgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG

EST: gi|93282364|gb|EB674628.1|EB674628

EST:     TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAG                         ATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG
genomic: TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAGgtaatcttat ... tgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG

EST: gi|91874225|gb|EB404182.1|EB404182

EST:     TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAG                         ATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG
genomic: TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAGgtaatcttat ... tgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG

EST: gi|211425716|gb|FL474991.1|FL474991

EST:     TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTG-TTTACCAG                         ATGGTCAGGCTAAGAGTAGTACTATTGAAAAGGGATTTGTAAGGATTTTGG
genomic: TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAGgtaatcttat ... tgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG

EST: gi|149055689|gb|EE156395.2|EE156395

EST:     AAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAG                         ATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG
genomic: AAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAGgtaatcttat ... tgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG

EST: gi|211477236|gb|FL318837.1|FL318837

EST:     TGCTAGGTTACTTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAG                         ATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG
genomic: TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAGgtaatcttat ... tgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG

EST: gi|86471499|gb|DY237869.1|DY237869

EST:     TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAG                         ATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG
genomic: TGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAGgtaatcttat ... tgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGG

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), 42 (downstream exon)
Score: 262

CCAACTCAAAAGGTTTTAGAACCTAATATTGTAGTTGGCGCACCATCGTCTGCTAGGTTACCTGAAGCTGGTAGTCAGTTAAATTGTGTTGTTTTACCAGgtaatcttat ... tgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGGATTCGATCTCTGCTCCCCCAGCTTTTGCAGGAGAGTTCCCATCTAACCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 289

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttcttacacctgtaaatagacattgatgacaaggtttttgtgttgtgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGGATTCGATCTCTGCTCCCCCAGCTTTTGCAGGAGAGTTCCCATCTAACCA

          tgtaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgacccactcatgtaggagcatttggcactgtgtctgtcctttttcttacacctgtaaatagacattgatgacaaggtttttgtgttgtgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGGATTCGATCTCTGCTCCCCCAGCTTTTGCAGGAGAGTTCCCATCTAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
catgacc
- - - - - -catgtag
- - - - - - - - - - gcatttg
- - - - - - - - - - - - - -gcactgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgttg