RetrogeneDB ID: retro_rnor_2874

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:139084786..139085144(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Chchd3
• Ensembl ID: ENSRNOG00000013211
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain-containing protein 3, mitochondrial [Source:RefSeq peptide;Acc:NP_001100058]

Sequence

>retro_rnor_2874
GAGAGGGCTGCAGTCAATGAGCAGTTACCAGAGCTATTATTTGTGAGGATATCCAGTGAGGAGGAACACTCAAAGGCAAA
GCATCCAGCTTGGCTGCTGGAAGAAAAGGTTAGGTGATAAGGAAGCAGGATGCTCTATCAAAGAGCAGCAGGTCAGATTG
GAGAGAAGCTCAGAGTTCTACAAAGTCATCACCTAGAAGTATCAGAATGCTGCTGAAGAGGTGGAATCAAAGTTCAAGCA
GTATCAATATCATCCAGATGAGTTACATCTGCAGACCAAGATGCTCCAGTGTTATCAGCAGGCTCTCAACTGATCTACTC
TGGACAGCTAATACATGGACTGTGTCAACCATCCCAAA

Alignment

ORF - retro_rnor_2874 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.94 %
• Parental protein coverage: 55.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKAVANEQLTRAILQERISSEENRTKVKHLARQLEEKDR-MIRKQDAF-YKEQLSRLEERSSEFYKVTTE
          E.A..NEQL....L..RISSEE...K.KH.A..LEEK.R..IRKQDA...KEQ..RL.ERSSEFYKV.T.
Retrocopy ERAAVNEQLPE-LLFVRISSEEEHSKAKHPAWLLEEKVR<VIRKQDAL<IKEQQVRL-ERSSEFYKVIT*

Parental  EYQKAAEEVESKFRRYEYHPVCADLQTKILQCYRQNTQQTLSCSALANQYMHCVNHAK
          .YQ.AAEEVESKF..Y.YHP....LQTK.LQCY....QQ.L..S.L...YM.CVNH.K
Retrocopy KYQNAAEEVESKFKQYQYHPDELHLQTKMLQCY----QQALN*STLDS*YMDCVNHPK

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	39.11 RPM
SRP017611_kidney	1.54 RPM	92.95 RPM
SRP017611_liver	0.00 RPM	34.22 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2874 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2874 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2874 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_3452

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001312	1 retrocopy	retro_cfam_374,
Dasypus novemcinctus	ENSDNOG00000004942	1 retrocopy	retro_dnov_2559,
Homo sapiens	ENSG00000106554	3 retrocopies	retro_hsap_358, retro_hsap_3759, retro_hsap_542,
Macaca mulatta	ENSMMUG00000001671	1 retrocopy	retro_mmul_14,
Mus musculus	ENSMUSG00000053768	1 retrocopy	retro_mmus_3452,
Nomascus leucogenys	ENSNLEG00000012967	3 retrocopies	retro_nleu_168, retro_nleu_716, retro_nleu_904,
Oryctolagus cuniculus	ENSOCUG00000014032	1 retrocopy	retro_ocun_801,
Pongo abelii	ENSPPYG00000025827	5 retrocopies	retro_pabe_2492, retro_pabe_3161, retro_pabe_345, retro_pabe_411, retro_pabe_501,
Pan troglodytes	ENSPTRG00000019711	4 retrocopies	retro_ptro_2550, retro_ptro_282, retro_ptro_407, retro_ptro_701,
Rattus norvegicus	ENSRNOG00000013211	1 retrocopy	retro_rnor_2874 ,
Sorex araneus	ENSSARG00000012111	1 retrocopy	retro_sara_592,
Ictidomys tridecemlineatus	ENSSTOG00000022282	1 retrocopy	retro_itri_1301,