RetrogeneDB ID:

retro_sara_399

Retrocopy
location
Organism:Shrew (Sorex araneus)
Coordinates:scaffold_193077:4334..4714(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PRDX1
Ensembl ID:ENSSARG00000004703
Aliases:None
Description:peroxiredoxin 1 [Source:HGNC Symbol;Acc:9352]


Retrocopy-Parental alignment summary:






>retro_sara_399
CCCCTTGACTTCACCTTTGTGTGCCCCATGAAAATCAATGCTTTCAGTGATAGGGCAGAAGAGCTTAAGAAACTCAACTT
CCTAGTGATTGGTGCTTCTGTAGATTCTCACTTTTGTCAGCTGACAAGGATCAATACACCCATGAAACAAAGAGGACTGA
GCCCCATGAACATTCCCTTTGTATCGGACCCTGAGCCAGCCATTGATTAGGATTATGGTTCTTAAAGGCTGATGAGGGCA
TCTCTTTCAGGGTTCATTGTATTATTGATGATAAGGGTATCCTTTGGCAGATCACTGTAAATAACCTCCCTGTTGGCCAC
TCCGTGAATGAAACACTAAGATTAACTCAGGCCCTCTAGCTCACTGATAAACATGGTGAA

ORF - retro_sara_399 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.56 %
Parental protein coverage: 74.27 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRAIAQ
PLDFTFVCP..I.AFSDRAEE.KKLN..VIGASVDSHFC.L..INTP.KQ.GL.PMNIP.VSDP..AI..
RetrocopyPLDFTFVCPMKINAFSDRAEELKKLNFLVIGASVDSHFCQLTRINTPMKQRGLSPMNIPFVSDPEPAID*
ParentalDYG-VLKADEGISFRGLFIIDDKGILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGE
DYG..LKADEGISFR...IIDDKGIL.QITVN.LPVG.SV.ETLRL.QA...TDKHGE
RetrocopyDYG<FLKADEGISFRVHCIIDDKGILWQITVNNLPVGHSVNETLRLTQAL*LTDKHGE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Sorex araneus was not studied using RNA-Seq expression data.
Sorex araneus was not studied using ChIP-Seq data.
Sorex araneus was not studied using EST data.
Sorex araneus was not studied using FANTOM5 data.
retro_sara_399 was not experimentally validated.

Retrocopy orthology:
Sorex araneus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 31 parental genes, and 85 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000136322 retrocopies
Bos taurus ENSBTAG000000036422 retrocopies
Canis familiaris ENSCAFG000000045675 retrocopies
Choloepus hoffmanni ENSCHOG000000033585 retrocopies
Ciona intestinalis ENSCING000000030021 retrocopy
Callithrix jacchus ENSCJAG000000048072 retrocopies
Cavia porcellus ENSCPOG000000141373 retrocopies
Dasypus novemcinctus ENSDNOG000000184881 retrocopy
Dipodomys ordii ENSDORG000000089751 retrocopy
Equus caballus ENSECAG000000086781 retrocopy
Echinops telfairi ENSETEG0000000792211 retrocopies
Felis catus ENSFCAG000000284841 retrocopy
Homo sapiens ENSG000001174501 retrocopy
Macropus eugenii ENSMEUG000000068204 retrocopies
Macaca mulatta ENSMMUG000000062211 retrocopy
Monodelphis domestica ENSMODG000000023822 retrocopies
Mus musculus ENSMUSG000000286915 retrocopies
Nomascus leucogenys ENSNLEG000000145242 retrocopies
Oryctolagus cuniculus ENSOCUG000000059512 retrocopies
Otolemur garnettii ENSOGAG000000023034 retrocopies
Pongo abelii ENSPPYG000000014111 retrocopy
Pan troglodytes ENSPTRG000000006751 retrocopy
Pteropus vampyrus ENSPVAG000000150011 retrocopy
Rattus norvegicus ENSRNOG000000171948 retrocopies
Sorex araneus ENSSARG000000001461 retrocopy
Sorex araneus ENSSARG00000004703 5 retrocopies
Sus scrofa ENSSSCG000000039141 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000234132 retrocopies
Tupaia belangeri ENSTBEG000000159974 retrocopies
Tarsius syrichta ENSTSYG000000110311 retrocopy
Tursiops truncatus ENSTTRG000000088584 retrocopies



Copyright © RetrogeneDB 2014-2017