Introduction

CarpBase: www.carpbase.org, is a database of Common Carp genome. CarpBase is open for everyone intresting it, so you could use all of the data, sequences, maps, etc. in site. But for some reason, part of datas of carp is not be avalible, one could contract us for demanding. Genome is show with GBrowse2.0, and one can click the menu "Browse" on the top to view them.

Start use this from home

A home link may like this, content menu is on the top, where you can find almost evething. Details of the munus' function is following.

home

Mainly we show the genetic maps in Genome View part. By clicking any of the chromosome, you could see a large picture with markers beside, like this.

genetic

A selector is on the top for changing to another chromosome. RED line will show the relative position on the chrom of a marker when sliding on the viewer. Each side of marker can be clicked and then browser will show it in GBrowse2.

Genome view with GBrowse

Genome browse may be seen in everywhere. Clicking the "Browse" top menu will start a quick lauch.

home

You can do many things in GBrowse. To know more infomation about gbrowse, goto website: http://gmod.org/wiki/GBrowse

QTL

The QTL data is consist of two parts: one is the qtl listed by traits or chromosomes( QTL topmenu -> QTL by trait, default page is following at left), one is the history data listing in four stage( QTL topmenu -> QTL by population, default page is following at right).

home home

QTL by trait

Default page of QTL by trait is simply grouped by traits name and show one of qtl for a trait. As see in the left, qtls of common carp is listed as Trait name, QTL name, Linkage Group, CI, LOD, PVE.

The "Trait name" column shows all the traits maintained. Click to each trait, a new page will be opened and listing the qtl names relevanced to the select trait.

QTL of one trait

Click "QTL" column will show qtl detail informations.

QTL infomation

Click "Linkage group" column will show qtl details in one linkage group.

QTL Linkage group

QTL by population

Default page of QTL by population is separated to four stage, each stage could be navigated directly with four sub menu of QTL -> QTL by Population.

QTL population sub menu

All items of the four stages have a independent page that displays detail information of population item. Samples are following here.

QTL 183a population QTL 183b population QTL 192a population

Synteny

The Synteny search can be used to find out relationships among genes from common carp and other species.

syntenty image

Resequencing

We aligned most short reads onto the NCBI human reference 36 and YH variants were identified while we built up YH consensus. from Songpu and Hebao

Re-sequencing

Annotation

Genes were assigned to a wide range of molecular functions by using Non-coding RNA, pathway, Interpro, Gene Ontology (GO), Transcription factor, Immune, gene family, orthologous group, and repeat analyses.

Annotation

Tools: Search and Blast

Blast, RepeatMasker, Sequence Search, gene search, domain search, BAC clone search and SSR tools are provided.

Tools

AS

Alternative Splicing information of common carp and other five fishes (Catfish, Zebrafish, Fugu, Medaka, Stickleback) are listed, according to different types, such as Exon Skipping, Alternative Donor site, Alternative Acceptor site, Alternative Position and Intron Retention.

Tools