RetrogeneDB ID: retro_mmus_3452

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:51753631..51753999(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Chchd3
• Ensembl ID: ENSMUSG00000053768
• Aliases: Chchd3, 0610041L09Rik, 1700039J09Rik, AW558177
• Description: coiled-coil-helix-coiled-coil-helix domain containing 3 [Source:MGI Symbol;Acc:MGI:1913325]

Sequence

>retro_mmus_3452
GAGAGGGCTGCAGTCAATGAGCAGTTAACCAGAGTTGTCATTTGGGAAAGGATATCCACTGAGGAGGAACACTCAAAGGC
AAAGCATCTGGTTTGGCAGCTGGAATGAAAGGCCAGGTGATAAGGAACCGCAGGATGCTCTATCAAAGAGCTGAAGGCCA
GACGGGAGAGAAGCTCGATTTCTACAAACTTATGACTGAGACATATCAGAAAGCCACTGAAGAGGTGAAAAAGTTCAAGC
ATCCAGATTGGCTACATCTGTAGACCAGGATCCTCCAGTGTTATCAGAAGGCTCTCAACTGATCTATTCTGTCCAGTTAA
TACAAGTACGGTGTCAACCATCCCAAACAGAGAATTCTGGAGAAAGGA

Alignment

ORF - retro_mmus_3452 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.35 %
• Parental protein coverage: 58.59 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ERAAANEQLTRAVLRERISSEEERMKAKHLARQLEEKDR-VMRKQDAFY-KEQLARLEERSS-EFYKVTT
          ERAA.NEQLTR.V..ERIS.EEE..KAKHL..QLE.K.R.V.R.....Y.KE..AR..ERSS..FYK..T
Retrocopy ERAAVNEQLTRVVIWERISTEEEHSKAKHLVWQLE*KAR<VIRNRRMLY>KELKAR-RERSS<DFYKLMT

Parental  EEYQKAAEEVEAKFKRYEYHPVCADLQTKILQCYRQNTQQTLSCSALASQYMHCVNHAKQSMLEKG
          E.YQKA.EEV..KFK....HP....L.T.ILQCY....Q..L..S.L.S.Y...VNH.KQ..LEKG
Retrocopy ETYQKATEEVK-KFK----HPDWLHL*TRILQCY----QKALN*SILSS*YKYGVNHPKQRILEKG

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
SRP007412_brain	0.00 RPM	34.32 RPM
SRP007412_cerebellum	0.00 RPM	40.34 RPM
SRP007412_heart	0.00 RPM	231.73 RPM
SRP007412_kidney	0.00 RPM	143.14 RPM
SRP007412_liver	0.00 RPM	70.29 RPM
SRP007412_testis	0.50 RPM	103.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3452 was not detected

EST

No EST(s) were mapped for retro_mmus_3452 retrocopy.

TSS

No TSS is located nearby retro_mmus_3452 retrocopy 5' end.

Lab

retro_mmus_3452 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3452 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2874

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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,