RetrogeneDB ID: retro_sara_320

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_162197:20059..20420(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRPEL2
• Ensembl ID: ENSSARG00000005467
• Aliases: None
• Description: GrpE-like 2, mitochondrial (E. coli) [Source:HGNC Symbol;Acc:21060]

Sequence

>retro_sara_320
GTCAGGAGGCAGCTGGCCTCGGGTGCACAGCACAGCGGCAGAGCTTGGCTGCACCCTTTCAGCACCGCCATCCAGTGAAC
CACCGATGAGGACTGCAGTTCGGAAGACCCTCCTGATGATCTTGGTCCTGCTCTTGCATAATGAGCCTTAAAGCTAAAAG
CTGTTAAGCTGGAGAAGGAAGTGCAGGATTTGATAATAAAATACCAGAGAGATGTAGCTGATGAGTAAAACATCAGAAGG
CGAACCCAGAGATGTGTGGAGGATGCCAAGATATTTGGAATTCAGAGTTTCTGTAAGGACTTCTGTGGAGGTGGCAGACA
CTTTGGAGAAGACAGCAGAGTGCCTTTCTGCAGAAGTAGAC

Alignment

ORF - retro_sara_320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 53.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRRLLASGARSGGRAWLHPFSTATQRTAGEDCSSEDPPDELGPSLAERALKLKAVKLEKEVQDLTIKYQR
          .RR.LASGA...GRAWLHPFSTA.Q.T..EDCSSEDPPD.LGP.LA..ALKLKAVKLEKEVQDL.IKYQR
Retrocopy VRRQLASGAQHSGRAWLHPFSTAIQ*TTDEDCSSEDPPDDLGPALA**ALKLKAVKLEKEVQDLIIKYQR

Parental  AVADGENIRRRTQRCVEDAKIFGIQSFCKDL-VEVADLLEKTAECLSAEAE
          .VAD..NIRRRTQRCVEDAKIFGIQSFCKD..VEVAD.LEKTAECLSAE..
Retrocopy DVADE*NIRRRTQRCVEDAKIFGIQSFCKDF>VEVADTLEKTAECLSAEVD

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_320 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004070	1 retrocopy	retro_chof_1984,
Dipodomys ordii	ENSDORG00000011142	1 retrocopy	retro_dord_353,
Felis catus	ENSFCAG00000003624	1 retrocopy	retro_fcat_618,
Homo sapiens	ENSG00000164284	2 retrocopies	retro_hsap_1284, retro_hsap_4842,
Gorilla gorilla	ENSGGOG00000005410	2 retrocopies	retro_ggor_1008, retro_ggor_3021,
Macaca mulatta	ENSMMUG00000021662	1 retrocopy	retro_mmul_1317,
Nomascus leucogenys	ENSNLEG00000010160	1 retrocopy	retro_nleu_710,
Oryctolagus cuniculus	ENSOCUG00000016138	3 retrocopies	retro_ocun_89, retro_ocun_905, retro_ocun_943,
Otolemur garnettii	ENSOGAG00000014326	1 retrocopy	retro_ogar_791,
Pongo abelii	ENSPPYG00000015933	2 retrocopies	retro_pabe_1063, retro_pabe_3764,
Pan troglodytes	ENSPTRG00000017396	2 retrocopies	retro_ptro_3226, retro_ptro_877,
Sorex araneus	ENSSARG00000005467	2 retrocopies	retro_sara_320 , retro_sara_511,