RetrogeneDB ID: retro_sara_75

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_2123:57481..57862(-)
• Located in intron of: ENSSARG00000010631

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA6
• Ensembl ID: ENSSARG00000003814
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6, 14kDa [Source:HGNC Symbol;Acc:7690]

Sequence

>retro_sara_75
AAGACGGCATCGAGAGGGCTCCGGTGGGCTTCTGTGGCAACCAGCACCTAGGTGAAGCCCATTTTCAGTCAGGACACAAA
TGAGGCCAGGCGGAGCATGTGCAGGCTCTACCAAGTCTGATATTGGGAGGTGCTGAACCCTGTGCACTTATTTCAGCTGG
ACATCACTGTGAAACAGAGTTGGGATAAAGTCTGAGAACTGTTTAAGAATGCCCACGTCACAGACCCCAGGGTGGTTGAT
CTGCTGATCATTAAGGGAAAGATGGAATTAGAGGAAATGACTGAAGCATGGAAGCAGCGGACACACGTTACACAGTTCCT
CCAAGAAACAGAAGTGCCACGGCCAAAGGATTTCCTGTCCAAGTTCCATATTGGCCATGAC

Alignment

ORF - retro_sara_75 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.88 %
• Parental protein coverage: 83.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMAASGLRRAAAATSTSVKPIFSRDMNEAKRRVRELYRAWYREVPNTVHLFQLDITVKQGRDKVREMFKK
          K.A..GLR.A..ATST.VKPIFS.D.NEA.R....LY...Y.EV.N.VHLFQLDITVKQ..DKV.E.F.K
Retrocopy KTASRGLRWASVATST*VKPIFSQDTNEARRSMCRLYQV*YWEVLNPVHLFQLDITVKQSWDKV*ELF-K

Parental  NAHVTDPRVVDLLVIKGKMELEETIKVWKQRTHVMRFFHETEAPRPKDFLSKFYIGHD
          NAHVTDPRVVDLL.IKGKMELEE....WKQRTHV..F..ETE.PRPKDFLSKF.IGHD
Retrocopy NAHVTDPRVVDLLIIKGKMELEEMTEAWKQRTHVTQFLQETEVPRPKDFLSKFHIGHD

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_75 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000001466	1 retrocopy	retro_csav_29,
Erinaceus europaeus	ENSEEUG00000004117	1 retrocopy	retro_eeur_664,
Monodelphis domestica	ENSMODG00000007030	1 retrocopy	retro_mdom_397,
Mus musculus	ENSMUSG00000022450	1 retrocopy	retro_mmus_2693,
Oryctolagus cuniculus	ENSOCUG00000015446	1 retrocopy	retro_ocun_1128,
Otolemur garnettii	ENSOGAG00000014762	2 retrocopies	retro_ogar_1656, retro_ogar_312,
Procavia capensis	ENSPCAG00000004570	1 retrocopy	retro_pcap_18,
Rattus norvegicus	ENSRNOG00000008569	1 retrocopy	retro_rnor_604,
Sorex araneus	ENSSARG00000003814	1 retrocopy	retro_sara_75 ,