RetrogeneDB ID: retro_rnor_2338

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:152603419..152603863(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000004262
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nucks1
• Ensembl ID: ENSRNOG00000047287
• Aliases: Nucks1, Nucks
• Description: Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9EPJ0]

Sequence

>retro_rnor_2338
ATGTCTCGGCCTGTCAGAAATAGGAAGGTCGTTGATTACTCACAGTTTCAGGAGTCAGATGATGCAGAGGGAGATTATGG
AAGAGATTCAGGCCCTCCTGCTAAGAAGATTCGGTCATCTCCCCGAGAGACTAAAAATAAGAGGCGATCTGGCAAAAATT
CACAAGAAGACAGTGAAGACTCAGAAGAAAAAGATGTGAAGAGCAAGAAGGATGATTCTCACTCAGCAGAAGACAGTGAA
GATGAAAAAGATGACCATAAAAGTGTACGCCAGCAGCGGCAGGCAGCATCGAAAGCAGCTTCTAAGCAGAGAGAGATGCT
CTTGGAAGATGTGGGCAGCGAGGAGGAGCCGGAAGAAGATGATGAGGCGTCATTCCAGGAGAAAGATTCTGGCAGCGACG
AAGATTTCCTAATGGAGGACGACGATGATAGTGATTATGGCAGT

Alignment

ORF - retro_rnor_2338 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.62 %
• Parental protein coverage: 60.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRPVRNRKVVDYSQFQESDDADEDYGRDSGPPAKKIRSSPREAKNKRRSGKNSQEDSEDSEEKDVKTKK
          MSRPVRNRKVVDYSQFQESDDA..DYGRDSGPPAKKIRSSPRE.KNKRRSGKNSQEDSEDSEEKDVK.KK
Retrocopy MSRPVRNRKVVDYSQFQESDDAEGDYGRDSGPPAKKIRSSPRETKNKRRSGKNSQEDSEDSEEKDVKSKK

Parental  DDSHSAEDSEDEKDDHKSVRQQRQAASKAASKQREMLLEDVGSEEEPEEDDEAPFQEKDSGSDEDFLMED
          DDSHSAEDSEDEKDDHKSVRQQRQAASKAASKQREMLLEDVGSEEEPEEDDEA.FQEKDSGSDEDFLMED
Retrocopy DDSHSAEDSEDEKDDHKSVRQQRQAASKAASKQREMLLEDVGSEEEPEEDDEASFQEKDSGSDEDFLMED

Parental  DDDSDYGS
          DDDSDYGS
Retrocopy DDDSDYGS

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	0.07 RPM	35.30 RPM
SRP017611_kidney	0.00 RPM	29.87 RPM
SRP017611_liver	0.00 RPM	13.25 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2338 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2338 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012950	1 retrocopy	retro_amel_339,
Bos taurus	ENSBTAG00000008001	1 retrocopy	retro_btau_541,
Choloepus hoffmanni	ENSCHOG00000001855	1 retrocopy	retro_chof_437,
Dasypus novemcinctus	ENSDNOG00000017212	2 retrocopies	retro_dnov_348, retro_dnov_6,
Dipodomys ordii	ENSDORG00000003183	1 retrocopy	retro_dord_688,
Homo sapiens	ENSG00000069275	1 retrocopy	retro_hsap_521,
Gorilla gorilla	ENSGGOG00000026655	1 retrocopy	retro_ggor_480,
Macropus eugenii	ENSMEUG00000007829	2 retrocopies	retro_meug_2015, retro_meug_372,
Macaca mulatta	ENSMMUG00000005645	1 retrocopy	retro_mmul_422,
Monodelphis domestica	ENSMODG00000001832	1 retrocopy	retro_mdom_980,
Nomascus leucogenys	ENSNLEG00000014564	1 retrocopy	retro_nleu_2576,
Pan troglodytes	ENSPTRG00000001904	1 retrocopy	retro_ptro_389,
Rattus norvegicus	ENSRNOG00000047287	2 retrocopies	retro_rnor_2337, retro_rnor_2338 ,
Tupaia belangeri	ENSTBEG00000015641	1 retrocopy	retro_tbel_2591,
Tarsius syrichta	ENSTSYG00000000910	1 retrocopy	retro_tsyr_987,
Vicugna pacos	ENSVPAG00000003751	1 retrocopy	retro_vpac_313,