RetrogeneDB ID: retro_rnor_1536

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:139701290..139701982(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rsrc2
• Ensembl ID: ENSRNOG00000001238
• Aliases: None
• Description: Arginine/serine-rich coiled-coil protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5PQR4]

Sequence

>retro_rnor_1536
AAGAGAATTGAAAAACCAAGAAGATTTAGCAGAAACCTAAGCCAAACACCTAGGGGACACCTACCTCCCTTCAGAGGCAG
AAACACAGCAATGGACACCCAAGAAGCTTAGCTAGGAGATTAGAACGGGCAAAGAAATTGCAAGAACAATGAGAAAAGAA
AATGGTTGGAAAACAAAAACAAGAAATAGCTGCAGCGGCTGCAGCCACTGAAGCTACTGTTCTTAATGTTGCTGCACTGT
TGGCAACAGGAACGTGGGTTACTCCTCAGACAGCTATAGCAGCTCAAATGTCAGTCCTGTGAGCTAAAGCCTTGGCAGAG
ACCAGCATAGTTGTGCCCAGCCACCATAACCCAGCAGCTGTGAATCTAGTGAAATTTGCTGAGCAAGAGAAAAAGAGGAA
AATGCTCTGGCAAGGCAAGGAAGAAGGCAACAGATCTTAGTCTGCTGAGATATGGGGAAAATTGAATTTTAGAAACAAGG
ACCAAAATGCCAAATTTAGGAAGTTAATGGGCATTAAGAGTGAAGGTGAAGCTGGCTGTAGCTCCCTTGATAAAGAAAGT
TACAAGATTTTGAAGCAACAAGAAGTTTTTCAAAATCTTGATGCTCAGTATGAATGGCAAGATTGCAAGTCCACACACGA
AGAGCAATGCGATTTGGGTTTCACGTCATCAATGCGTGAAATGAATACGGTT

Alignment

ORF - retro_rnor_1536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.39 %
• Parental protein coverage: 61.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KRIEKPRRFSRSLSRTPSP--PPFRGRNTAMDAQEA-LARRLERAKKLQEQREKEMVEKQKQQEMAAAAA
          KRIEKPRRFSR.LS.TP....PPFRGRNTAMD.QEA.LARRLERAKKLQEQ.EK.MV.KQKQ.E.AAAAA
Retrocopy KRIEKPRRFSRNLSQTPRGHLPPFRGRNTAMDTQEA<LARRLERAKKLQEQ*EKKMVGKQKQ-EIAAAAA

Parental  ATGGSVLNVAALLASGTQVTPQIAMAAQMAALQAKALAETGIAVPSYYNPAAVNPMKFAEQEKKRKMLWQ
          AT...VLNVAALLA.GT.VTPQ.A.AAQM..L.AKALAET.I.VPS..NPAAVN..KFAEQEKKRKMLWQ
Retrocopy ATEATVLNVAALLATGTWVTPQTAIAAQMSVL*AKALAETSIVVPSHHNPAAVNLVKFAEQEKKRKMLWQ

Parental  GKKEGDKSQSAEIWEKLNFGNKDQNVKFRKLMGIKSEDEAGCSSVDEESYKTLKQQEEVFRNLDAQYE-M
          GK.EG..S.SAEIW.KLNF.NKDQN.KFRKLMGIKSE.EAGCSS.D.ESYK.LKQQ.EVF.NLDAQYE.M
Retrocopy GKEEGNRS*SAEIWGKLNFRNKDQNAKFRKLMGIKSEGEAGCSSLDKESYKILKQQ-EVFQNLDAQYE<M

Parental  ARSQTHTQRGM-GLGFTSSMRGMDTV
          AR.Q.HT.R.M..LGFTSSMR.M.TV
Retrocopy ARLQVHTRRAM>DLGFTSSMREMNTV

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	47.95 RPM
SRP017611_kidney	0.00 RPM	41.24 RPM
SRP017611_liver	0.00 RPM	20.78 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1536 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1536 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1536 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020419	1 retrocopy	retro_cjac_468,
Dasypus novemcinctus	ENSDNOG00000008912	1 retrocopy	retro_dnov_303,
Macaca mulatta	ENSMMUG00000004412	1 retrocopy	retro_mmul_1179,
Mus musculus	ENSMUSG00000029422	1 retrocopy	retro_mmus_2465,
Rattus norvegicus	ENSRNOG00000001238	1 retrocopy	retro_rnor_1536 ,