RetrogeneDB ID: retro_rnor_1978

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:142283641..142283932(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Atp5d
• Ensembl ID: ENSRNOG00000014625
• Aliases: None
• Description: ATP synthase subunit delta, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_620806]

Sequence

>retro_rnor_1978
TTGGCATCTCATGTCCCCACACTACAGGTCCTACGGCCTGGGCTGGTAGTGGTTCACGTGGAAGACAGCACCACAACTAA
GTATTTTGTGAGCATCGGCTCCATCACTGTGAACTCGGACTCCTCTGTGCAATTACTAGCTGAAGAAGCTGTGACACTGG
ACAACCTGGAGGCAGCCCGGGCCAACCTGGAGAAGGTGCAGTCAGAACTGTCAAGTGCAGCAGATGAGGCAGCAGGGGCT
GAGATTCAAGTCAGTATTGAGGCCAATGAAGCCCTAGTGAAGGCACTGGAG

Alignment

ORF - retro_rnor_1978 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.85 %
• Parental protein coverage: 58.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LASHVPTLQVLRPGLVVVHAEDGTTTKYFVSSGSVTVNADSSVQLLAEEVVTLDMLDLGAARANLEKAQS
          LASHVPTLQVLRPGLVVVH.ED.TTTKYFVS.GS.TVN.DSSVQLLAEE.VTLD.L...AARANLEK.QS
Retrocopy LASHVPTLQVLRPGLVVVHVEDSTTTKYFVSIGSITVNSDSSVQLLAEEAVTLDNLE--AARANLEKVQS

Parental  ELSGAADEAARAEIQIRIEANEALVKALE
          ELS.AADEAA.AEIQ..IEANEALVKALE
Retrocopy ELSSAADEAAGAEIQVSIEANEALVKALE

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	103.67 RPM
SRP017611_kidney	0.00 RPM	172.78 RPM
SRP017611_liver	0.00 RPM	72.95 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1978 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1978 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1978 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002168	1 retrocopy	retro_acar_96,
Microcebus murinus	ENSMICG00000014960	1 retrocopy	retro_mmur_1137,
Monodelphis domestica	ENSMODG00000005314	1 retrocopy	retro_mdom_1079,
Rattus norvegicus	ENSRNOG00000014625	1 retrocopy	retro_rnor_1978 ,