RetrogeneDB ID: retro_rnor_1436

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:64014917..64015248(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000049040
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nhp2
• Ensembl ID: ENSRNOG00000004247
• Aliases: None
• Description: NHP2 ribonucleoprotein homolog [Source:RefSeq peptide;Acc:NP_001099249]

Sequence

>retro_rnor_1436
CGCCTGACGTACAAGCTCTACAGATGCATGAAGAAGGTCGTGAAACAGAAGCAGATTTGTCACAGGGTGGAGGAAGTCAG
AAATGTGTCAACAAGGGCAAGAAAGGGATCATGGTTTTGGCAGAAGATACATGGCTGATTGAGGTGTACTGCCACCTTCC
AGTTGTGTGGAGAAACAGAATTTGCCCTACGTCTACATTCTCTCTAAGTCGGACTTGGGAGCAGCTACAGACTCCAAGTG
TCCCACTTGTGTGCTCACGGTGAAGCCCCATGAAGATCAGGAGGCCAATGACGAGTACCTGGAGGAGGTTCAGGCACAGC
CTACACCCCTG

Alignment

ORF - retro_rnor_1436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.56 %
• Parental protein coverage: 73.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLTRKLYKCIKKAVKQKQIRRGVKEV-QKFVNKGEKGIMVLAGDTLPIEVYCHLPVM-CEDQNLPYVYIP
          RLT.KLY.C.KK.VKQKQI...V.EV.QK.VNKG.KGIMVLA.DT..IEVYCHLPV...E.QNLPYVYI.
Retrocopy RLTYKLYRCMKKVVKQKQICHRVEEV<QKCVNKGKKGIMVLAEDTWLIEVYCHLPVV<VEKQNLPYVYIL

Parental  SKTDLGAATGSKRPTCVIMVKPHEDYQEAYDKCLEEVQALPTPL
          SK.DLGAAT.SK.PTCV..VKPHED.QEA.D..LEEVQA.PTPL
Retrocopy SKSDLGAATDSKCPTCVLTVKPHED-QEANDEYLEEVQAQPTPL

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1436 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1436 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1436 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012244	1 retrocopy	retro_cjac_264,
Homo sapiens	ENSG00000145912	2 retrocopies	retro_hsap_3712, retro_hsap_611,
Gorilla gorilla	ENSGGOG00000000015	1 retrocopy	retro_ggor_2509,
Macropus eugenii	ENSMEUG00000003839	2 retrocopies	retro_meug_285, retro_meug_320,
Macaca mulatta	ENSMMUG00000018757	1 retrocopy	retro_mmul_1702,
Monodelphis domestica	ENSMODG00000004231	1 retrocopy	retro_mdom_345,
Mus musculus	ENSMUSG00000001056	1 retrocopy	retro_mmus_565,
Oryctolagus cuniculus	ENSOCUG00000016057	1 retrocopy	retro_ocun_151,
Ochotona princeps	ENSOPRG00000007907	3 retrocopies	retro_opri_305, retro_opri_421, retro_opri_810,
Pongo abelii	ENSPPYG00000016105	3 retrocopies	retro_pabe_1704, retro_pabe_3143, retro_pabe_481,
Rattus norvegicus	ENSRNOG00000004247	2 retrocopies	retro_rnor_1436 , retro_rnor_2198,
Sus scrofa	ENSSSCG00000014032	1 retrocopy	retro_sscr_407,