ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GAAACTTTCATCTCCAAACTTCAAGGTTGATGGGAGCCAGTTGACTGTTAGTTGGGCTGAACCTAAGGGTTCAACAGATGCTTCATCTGCAGCTGCTCAGgtagacatttgggctaaaaattcaaattcaaattctattgtattgttatatttcaatttttaggccttttggttttgcaatgataggcttgtgcaagtct...

Basic information

species	Zea mays
transcript	GRMZM2G103430_T04
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G103430_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g14430.2 (Oryza sativa), 5'ss of exon 5

GAAACTTTCATCTCCAAACTTCAAGGTTGATGGGAGCCAGTTGACTGTTAGTTGGGCTGAACCTAAGGGTTCAACAGATGCTTCATCTGCAGCTGCTCAGgtagacatttgggctaaaaattcaaattcaaattctattgtattgttatatttcaatttttaggccttttggttttgcaatgataggcttgtgcaagtct---
|||| | ||| | |||||||| ||||||||||| ||||| ||||| || || ||||||||||||||||||||| ||||| |||| ||||||||||| ||||||    |      | ||||   |||   |      | | ||   |   |||   |   |||   ||  |   | |  || |    | |||  |    ||   
GAAATTGTCAGCACCAAACTTTAAGGTTGATGGTAGCCAATTGACCGTCAGCTGGGCTGAACCTAAGGGTTCATCAGATTCTTCTTCTGCAGCTGCCCAGgtatctttactatatgaaaaga-aaacctattggtgaatctaccatc-cattagtacccttatctctacta-ctataaaaagcagagtttgctctgcccttcc

upper sequence: GRMZM2G103430_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g06130.2 (Oryza sativa), 5'ss of exon 5

GAAACTTTCATCTCCAAACTTCAAGGTTGATGGGAGCCAGTTGACTGTTAGTTGGGCTGAACCTAAGGGTTCAAC------AGATGCTTCATCTGCAGCTGCTCAGgtagacatttgggctaaaaattcaaa----ttcaaattctattgtattgttatatttcaatttttaggccttttggttttgcaatgataggcttgtgcaagtct
       ||| | |||||||| ||||||||||| ||||||||||| || || ||||||||||||||||||||| |      |||| |||| ||||||||||| |||||| ||| |     | |||| |||      |  |   || |  |      |  |  ||      | |  ||   |    |      | |    |||  |     
------GTCAGCACCAAACTTTAAGGTTGATGGTAGCCAGTTGACCGTCAGCTGGGCTGAACCTAAGGGTTCATCATCATCAGATTCTTCTTCTGCAGCTGCCCAGgtatacactgtaaatgaaaagtcagcgctttctatgctcaacggatgcactgcagctctgcaaattgaactagggtcccttgggaaaaaaaactgtttat----

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|40336436|gb|CK370506.1|CK370506

EST:     GTTGGGCTGAACCTAAGGGTTCAACAGATGCTTCATCTGCAGCTGCTCAG                         GTGAAGACTATATATGTGTAGAACCTACCTGAAAATGTTTCTAAAGAGAAG
genomic: GTTGGGCTGAACCTAAGGGTTCAACAGATGCTTCATCTGCAGCTGCTCAGgtagacattt ... aattactcagGTGAAGACTATATATGTGAAGAACCTACCTGAAAATGTTTCTAAAGAGAAG

EST: gi|28910015|gb|CB331214.1|CB331214

EST:     GTTGGGCTGAACCTAAGGGTTCAACAGATGCTTCATCTGCAGCTGCTCAG                         GTGAAGACTATATATGTGAAGAACCTACCTGAAAATGTTTCTAAAGAGAAG
genomic: GTTGGGCTGAACCTAAGGGTTCAACAGATGCTTCATCTGCAGCTGCTCAGgtagacattt ... aattactcagGTGAAGACTATATATGTGAAGAACCTACCTGAAAATGTTTCTAAAGAGAAG

EST: gi|20811268|gb|BQ295746.1|BQ295746

EST:     GTTGGGCTGAACCTAAGGG-TCAACAGATGCTTCATCTGCAGCTGCTCAG                         GTGAAGACTATATATGTGAAGAACCTACCTGAAAATGTTTCTAAAGAGAAG
genomic: GTTGGGCTGAACCTAAGGGTTCAACAGATGCTTCATCTGCAGCTGCTCAGgtagacattt ... aattactcagGTGAAGACTATATATGTGAAGAACCTACCTGAAAATGTTTCTAAAGAGAAG

EST: gi|37393328|gb|CF633926.1|CF633926

EST:     TGCAGCTGCTCAG                         GTGAAGACTATATATGTGTAGAACCTACCTGAAAATGTTTCTAAAGAGAAG
genomic: TGCAGCTGCTCAGgtagacattt ... aattactcagGTGAAGACTATATATGTGAAGAACCTACCTGAAAATGTTTCTAAAGAGAAG

EST: gi|148930063|gb|EE285990.2|EE285990

EST:     GGTTCAACAGATGCTTCATCTGCAGCTGCTCAG                         GTGAGGACTATATATGTGAAGAACCTACCTGAAAATG-TTCTAAAGAGAAG
genomic: GGTTCAACAGATGCTTCATCTGCAGCTGCTCAGgtagacattt ... aattactcagGTGAAGACTATATATGTGAAGAACCTACCTGAAAATGTTTCTAAAGAGAAG

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), 47 (downstream exon)
Score: 60

GAAACTTTCATCTCCAAACTTCAAGGTTGATGGGAGCCAGTTGACTGTTAGTTGGGCTGAACCTAAGGGTTCAACAGATGCTTCATCTGCAGCTGCTCAGgtagacattt ... aattactcagGTGAAGACTATATATGTGAAGAACCTACCTGAAAATGTTTCTAAAGAGAAGATAAAGGACCTGTTTGACAAACATGGAGAGGTCACAAAAATCGTTCTGC

Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 23

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 20

Block sizes: 48 (upstream exon), 29 (downstream exon)
Score: 6

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAACTTTCATCTCCAAACTTCAAGGTTGATGGGAGCCAGTTGACTGTTAGTTGGGCTGAACCTAAGGGTTCAACAGATGCTTCATCTGCAGCTGCTCAGgtagacatttgggctaaaaattcaaattcaaattctattgtattgttatatttcaatttttaggccttttggttttgcaatgataggcttgtgcaagtct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT