RetrogeneDB ID: retro_sara_368

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_181240:7258..7563(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: FRG1
• Ensembl ID: ENSSARG00000002471
• Aliases: None
• Description: FSHD region gene 1 [Source:HGNC Symbol;Acc:3954]

Sequence

>retro_sara_368
GCTCTGAAAAATGGCTTTATTCTTTTTACACTAGGAATTACACCTCGAGATTTTGATGGGCAGCCACTTCCTTCAGAGTA
GTTTACACCTGCCAAATTGTCTGATTCCAGAATTGCCCTGAAATCTGGCAATGAAAAATGCCTTGGTATAAATTCAGATG
GATTTATTGGACATTCAGATTCAATTGAACCAAAAGAATGACAGGAACCAGGCTTTCAAGATGGAAAATTACTTTACTAT
CCTCAACTAGCTGCTTTATTAGACACAATGAAGCAGGAGCTGCAGAAGCGAAAAGCAGAATAGCA

Alignment

ORF - retro_sara_368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.54 %
• Parental protein coverage: 53.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALDNG--LFTLGAPHKEVDEGPSPPEQFT-AVSSDSRIALKSGYGKYLGINSDGLVVGRSDAIGPREQWE
          AL.NG..LFTLG......D..P.P.E.FT.A..SDSRIALKSG..K.LGINSDG...G.SD.I.P.E..E
Retrocopy ALKNGFILFTLGITPRDFDGQPLPSE*FTPAKLSDSRIALKSGNEKCLGINSDGFI-GHSDSIEPKE*QE

Parental  PVFQDGKM-ALLASNSCFIRCNEAGDIEAKSKTA
          P.FQDGK...LL.S.SCFIR.NEAG..EAKS..A
Retrocopy PGFQDGKL<TLLSSTSCFIRHNEAGAAEAKSRIA

Legend:

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

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_368 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013503	1 retrocopy	retro_amel_1609,
Canis familiaris	ENSCAFG00000007135	1 retrocopy	retro_cfam_718,
Felis catus	ENSFCAG00000025737	1 retrocopy	retro_fcat_464,
Myotis lucifugus	ENSMLUG00000023179	2 retrocopies	retro_mluc_1185, retro_mluc_1490,
Rattus norvegicus	ENSRNOG00000009846	1 retrocopy	retro_rnor_88,
Sorex araneus	ENSSARG00000002471	1 retrocopy	retro_sara_368 ,
Tupaia belangeri	ENSTBEG00000014491	2 retrocopies	retro_tbel_1202, retro_tbel_3435,
Tarsius syrichta	ENSTSYG00000010985	2 retrocopies	retro_tsyr_1347, retro_tsyr_1778,