RetrogeneDB ID: retro_rnor_2925

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:60883260..60884026(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000003115
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nadkd1
• Ensembl ID: ENSRNOG00000016691
• Aliases: Nadk2, Nadkd1, RGD1306809
• Description: NAD kinase domain-containing protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q1HCL7]

Sequence

>retro_rnor_2925
GAAGGCTCAAGCTACAGTGGGTTACTTGAGCGACATCATATCCACACCAAAAATGTAGAACACATAATTGATAGTTTATG
GGATAAAGGGATTGAGGTGCACCTGGTAAAGCAGAGAGAGTACAATGAAGAGACTGTTAGATGGGCAGATGCTGTCATAG
CCACAGGAGGTGTTGGCATGATGCTTCTGACCGGCAGTAATTTCTGGACAGACTTAAACTTGTCATTGGGTCAACATTGA
TCAGGACCAGTCTGAAGGTCATTTATGTCTGCCTGTGCGATACACACATTCCTTTCCCAAAGCCTTACAGAAGTTCTTGC
GTGGTGAGTTCAGGTGGTTATGGAGGCAGCAGATCAGGTTATATCTGGAAGGGATCGTCATCAACCCCACTCCCGTGGAC
ATTCACGAACAGCAGCTGAGCTTGAATCAGCACAGTCAAGCCTTTAACATCGAAAGAGTGAATGATGAAAGATCTGAGGC
TTCAGGACCTCAGCTTCTGCCAGTGAGAGCACTCAACAAAGTCTTCATTGGGGAGAGCCTGTCATCCAAGGCTTCTAACT
ATGAAATTTCAGTTGATGATGGCCCATGGGAGAAGCAGAAGAGTTCAGGGCTCAATTTGTGTCCTGGAATAGGATCGAAG
GCCTGGTCCTTCAATATTAACAGGGTTGCAGCGCAGGCCCTTGAAGATGTTTTAAATTTTGCCAGACGACAAGGAAATCT
GACTCTTCCATTGAACAAAGAATTGGAACAAAGAAAAAGTAACAAA

Alignment

ORF - retro_rnor_2925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.72 %
• Parental protein coverage: 60.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KGSSYSGLLERHHIHTKNVEHIIDSLRDEGIEVRLVKRREYDEETVRWADAVIAAGGDGTMLLAASKV-L
          .GSSYSGLLERHHIHTKNVEHIIDSL.D.GIEV.LVK.REY.EETVRWADAVIA.GG.G.MLL..S...L
Retrocopy EGSSYSGLLERHHIHTKNVEHIIDSLWDKGIEVHLVKQREYNEETVRWADAVIATGGVGMMLLTGSNF<L

Parental  DRLKPVIG-VNTDPERSEGHLCLPVRYTHSFPEALQKFSRGEFRWLWRQRIRLYLEGTGINPSPVDLHEQ
          DRLK.VIG.VN.D...SEGHLCLPVRYTHSFP.ALQKF.RGEFRWLWRQ.IRLYLEG..INP.PVD.HEQ
Retrocopy DRLKLVIG<VNIDQDQSEGHLCLPVRYTHSFPKALQKFLRGEFRWLWRQQIRLYLEGIVINPTPVDIHEQ

Parental  QLSLNQHSRAFNIERVDDERSEASGPQLLPVRALNEVFIGESLSSRASYYEISVDDGPWEKQKSSGLNLC
          QLSLNQHS.AFNIERV.DERSEASGPQLLPVRALN.VFIGESLSS.AS.YEISVDDGPWEKQKSSGLNLC
Retrocopy QLSLNQHSQAFNIERVNDERSEASGPQLLPVRALNKVFIGESLSSKASNYEISVDDGPWEKQKSSGLNLC

Parental  TGTGSKAWSFNINRVAAQAVEDVLNIARRQGNLTLPLNKELVEKVTNE
          .G.GSKAWSFNINRVAAQA.EDVLN.ARRQGNLTLPLNKEL.....N.
Retrocopy PGIGSKAWSFNINRVAAQALEDVLNFARRQGNLTLPLNKELEQRKSNK

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	47.31 RPM
SRP017611_kidney	0.00 RPM	21.91 RPM
SRP017611_liver	0.00 RPM	200.30 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2925 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2925 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
Nomascus leucogenys	ENSNLEG00000016064	1 retrocopy	retro_nleu_3046,
Ochotona princeps	ENSOPRG00000009281	1 retrocopy	retro_opri_595,
Pongo abelii	ENSPPYG00000015401	1 retrocopy	retro_pabe_3323,
Rattus norvegicus	ENSRNOG00000016691	1 retrocopy	retro_rnor_2925 ,