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

...tgctgcatgattttcttaatctgaaggtcgtagctgatagaaaatcaataaggaatgagaacttctagtgtcagatgtttaaattgttttgtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGAACTCCATGACCTCTTGAGCAAGCCATCTTTGACCGGGATTCCGTTACTA

Basic information

species	Zea mays
transcript	GRMZM2G081622_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 3

-------------tgctgcatgattttcttaatctgaaggtcgtagctgatagaaaatcaataaggaatgagaacttctagtgtcagatgtttaaattgttttgtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGAACTCCATGACCTCTTGAGCAAGCCATCTTTGACCGGGATTCCGTTACTA
             || | | |  || | ||| | |     |||| |||| | | ||   |||      |   |||      ||    ||||||          ||| ||||||||||||||| || || || |||||||| |||||||| ||||| ||  | || |||||||| ||  |||||||||| |||||||| ||||| || ||||||
tccccttaaaatctggttcgttgttatattattttatttttcgttgctggtggcaa--taattgactttacaaacc----atggggaatgttttgg-------gttcctgcagGTATGTTGTGGATGCAGCCGATCGAGAGAACATGGCTATTGCCAAAAGCGAGCTCCATGATCTTCTGAGCAAGCCTTCTTTGACTGGGATCCCATTACTA

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|211286502|gb|FL423661.1|FL423661

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|116823538|gb|EC867078.1|EC867078

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAGAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|71310462|gb|DR791536.1|DR791536

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|13237001|gb|BG355015.1|BG355015

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|5296276|gb|AI783046.1|AI783046

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|6865359|gb|AW360709.1|AW360709

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|32794190|gb|CD946426.1|CD946426

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|211212173|gb|FL397456.1|FL397456

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|71434589|gb|DR815639.1|DR815639

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|71310460|gb|DR791535.1|DR791535

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|67015039|gb|CO443788.1|CO443788

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|5846813|gb|AI999896.1|AI999896

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|149086640|gb|EE176182.2|EE176182

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|148949509|gb|EC894973.2|EC894973

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|78105314|gb|DV523732.1|DV523732

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|78022902|gb|DV491289.1|DV491289

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|78081076|gb|DV509488.1|DV509488

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|14203624|gb|BG837301.1|BG837301

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|32862706|gb|CF002388.1|CF002388

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|9566365|gb|BE475874.1|BE475874

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|76283087|gb|DV022655.1|DV022655

EST:     AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: AGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

EST: gi|37392828|gb|CF633667.1|CF633667

EST:     ATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGT                         GTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA
genomic: ATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGA

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: 98

TTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCCAACCAAGATTCCGCAGCATGTGGGAGAGATACTGCCGTGCGGTTTCTGCAATTGTgtatgtattc ... gtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGAACTCCATGACCTCTTGAGCAAGCCATCTTTGACCGGGATTCCGTTACTA

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 80

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 113

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 86

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

caataaggaatgagaacttctagtgtcagatgtttaaattgttttgtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGAACTCCATGACCTCTTGAGCAAGCCATCTTTGACCGGGATTCCGTTACTA

                                         ttttgtttct  CT-rich tract
                                tttaaattgttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgcatgattttcttaatctgaaggtcgtagctgatagaaaatcaataaggaatgagaacttctagtgtcagatgtttaaattgttttgtttctgcagGTATGTTGTTGACGCGGCAGATCGAGAAAACATGGCCATTGCAAAGGGGGAACTCCATGACCTCTTGAGCAAGCCATCTTTGACCGGGATTCCGTTACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- -tgcatga
- - - - - - - - - - - - - - -gtagctg
- - - - - - - - - - - - - - - - - - atagaaaa