ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GCCTTTGTAAGGACAAAGGAAAATGCGGAGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagttacttacccctcttctaaaaaaacttatctgtgtcttgcactattcctggagtccagaatgtgttctttattttcaatgttgtagctgctg...

Basic information

species	Zea mays
transcript	GRMZM2G178227_T02
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G178227_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g50850.1 (Oryza sativa), 5'ss of exon 9

GCCTTTGTAAGGACAAAGGAAAATGCGGAGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagttacttacccctcttctaaaaaaacttatctgtgtcttgcactattcctggagtccagaatgtgttct-----ttattttcaatgttgtagctgctg
  | ||||| |||||||||||||||| ||||||||||| ||| | ||||||||||| |||||||||||||| |||||||||||  |  |   | |||||||    |||  ||  | | ||   ||||  |  ||  ||    |||||            | || ||   |  |  |  |  | 
ATCATTGTACGGACAAAGGAAAATGCAGAGAAGAAGCTGACTCTCACATATGAAGAAATGGAAGCAGAACGAGAAGAGgtaatctgc-atgcagccctctt----aaattctgttttctgatctgcaaaaggccctgatagtagaataaaggtcaaaggtcatgttgggtcatacatttttta

upper sequence: GRMZM2G178227_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv16s0098g00320.t01 (Vitis vinifera), 5'ss of exon 9

GCCTTTGTAAGGACAAAGGAAAATGCGGAGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagttacttacccctcttctaaaaaaacttatctgtgtcttgcactattcctggagtccagaatgtgttctttattttcaatgttgtagctgctg---
 |  | ||  | ||||| ||||||   |||||||| |   ||||||||||||| || |||||||||||||| ||||||||| ||  || ||| ||| | || |         |     | ||||   || || | |  ||        |  |||  | ||||  |||   |    |     
ACTATCGTGCGAACAAAAGAAAATATCGAGAAGAAACAGGCTTTGACATATGAGGAAATGGAAGCAGAACGTGAAGAGgtagtt--ttgcttcccctttttatttgtttttcttctcatatctttttctttttcagttgtttttttcct-ctctagaatttccttgtcaaaatccccatcc

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|61117876|gb|DN558837.1|DN558837

EST:     AGAAGAAGCTTACTTTGACATATGAAGAGACGGAAGCAGAACGGGAAGAG                         GAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC
genomic: AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC

EST: gi|31358406|gb|CD442763.1|CD442763

EST:     AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAG                         GANGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAAGCA-CAAATCTA
genomic: AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGA-GCAACAAATCTA

EST: gi|61117872|gb|DN558833.1|DN558833

EST:     GAAGAAGC-TACTNNTGACATATGAAGAGATGGAAGCAGAACGGGAAGAG                         GAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC
genomic: GAAGAAGCTTACT-TTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC

EST: gi|26456323|gb|CA827906.1|CA827906

EST:     AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAG                         GAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGC
genomic: AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGC

EST: gi|61117874|gb|DN558835.1|DN558835

EST:     AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAG                         GAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC
genomic: AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC

EST: gi|61117875|gb|DN558836.1|DN558836

EST:     AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAG                         GAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC
genomic: AGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTAC

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: 188

GCCTTTGTAAGGACAAAGGAAAATGCGGAGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagtt ... ttttctatagGAGGAGGTACAAGTTGACACTGAGAGTGATGACGAAGAGCAACAAATCTACAATCCTCTCAAGTTGCCGATGGGTTGGGATGGCAAACCTATCCCCTACT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 161

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTTTGTAAGGACAAAGGAAAATGCGGAGAAGAAGCTTACTTTGACATATGAAGAGATGGAAGCAGAACGGGAAGAGgtaattagttacttacccctcttctaaaaaaacttatctgtgtcttgcactattcctggagtccagaatgtgttctttattttcaatgttgtagctgctg

- - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA