RetrogeneDB ID: retro_mmus_1843

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:3732093..3732340(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ndufa3
• Ensembl ID: ENSMUSG00000035674
• Aliases: Ndufa3, 1010001M12Rik, 1700022J01Rik
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3 [Source:MGI Symbol;Acc:MGI:1913341]

Sequence

>retro_mmus_1843
GCTGGGAGATTCTCCACTGTCCTCAGAAATGTCTGCACAGAGAAACCAGTGCTGTGGCGTCCGTCACCACTGGGAACCTC
ACTATAATTATGCCCTAACTTAGCTTCTAACCAAGTAGGCCACCATAAGCGAACCGGCCACACCCCACAATTACTCAGTG
CTTATGAGAGATAATAGGAACATGCCTGATGTGGCCAGCCACCCCCAGGACCCTCAGGGCCCAAACCTGGAATGGCTGAA
GAACCTG

Alignment

ORF - retro_mmus_1843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.29 %
• Parental protein coverage: 98.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGRISAFLKNAWAKEPVL-VVSFSVWGLAIIMPMIS-PYTKYASMINKATPYNYPVPVRDDGNMPDVPSH
          AGR.S..L.N.....PVL.V.S.....L.IIMP..S...TK.A.....ATP.NY.V..RD..NMPDV.SH
Retrocopy AGRFSTVLRNVCTEKPVL<VASVTTGNLTIIMP*LS<LLTK*ATISEPATPHNYSVLMRDNRNMPDVASH

Parental  PQDPLGPSLDWLKNL
          PQDP.GP.L.WLKNL
Retrocopy PQDPQGPNLEWLKNL

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	49.62 RPM
SRP007412_cerebellum	0.00 RPM	51.80 RPM
SRP007412_heart	0.00 RPM	241.66 RPM
SRP007412_kidney	0.00 RPM	93.84 RPM
SRP007412_liver	0.00 RPM	66.82 RPM
SRP007412_testis	0.05 RPM	19.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1843 was not detected

EST

No EST(s) were mapped for retro_mmus_1843 retrocopy.

TSS

No TSS is located nearby retro_mmus_1843 retrocopy 5' end.

Lab

retro_mmus_1843 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1843 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 62 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007754	2 retrocopies	retro_btau_207, retro_btau_986,
Canis familiaris	ENSCAFG00000002703	4 retrocopies	retro_cfam_1103, retro_cfam_12, retro_cfam_1274, retro_cfam_695,
Callithrix jacchus	ENSCJAG00000018518	5 retrocopies	retro_cjac_188, retro_cjac_2215, retro_cjac_2526, retro_cjac_382, retro_cjac_92,
Cavia porcellus	ENSCPOG00000021937	1 retrocopy	retro_cpor_991,
Equus caballus	ENSECAG00000015897	3 retrocopies	retro_ecab_253, retro_ecab_598, retro_ecab_834,
Felis catus	ENSFCAG00000003611	6 retrocopies	retro_fcat_122, retro_fcat_1501, retro_fcat_442, retro_fcat_448, retro_fcat_839, retro_fcat_916,
Gorilla gorilla	ENSGGOG00000023650	2 retrocopies	retro_ggor_100, retro_ggor_1166,
Loxodonta africana	ENSLAFG00000018014	2 retrocopies	retro_lafr_225, retro_lafr_459,
Macropus eugenii	ENSMEUG00000002939	2 retrocopies	retro_meug_408, retro_meug_688,
Monodelphis domestica	ENSMODG00000004118	1 retrocopy	retro_mdom_404,
Mustela putorius furo	ENSMPUG00000010317	3 retrocopies	retro_mputfur_1070, retro_mputfur_124, retro_mputfur_771,
Mus musculus	ENSMUSG00000035674	3 retrocopies	retro_mmus_1843 , retro_mmus_3244, retro_mmus_486,
Otolemur garnettii	ENSOGAG00000006931	10 retrocopies	retro_ogar_1056, retro_ogar_1244, retro_ogar_1260, retro_ogar_1990, retro_ogar_2128, retro_ogar_2732, retro_ogar_2970, retro_ogar_3105, retro_ogar_3427, retro_ogar_729,
Pan troglodytes	ENSPTRG00000028890	5 retrocopies	retro_ptro_1032, retro_ptro_1093, retro_ptro_1336, retro_ptro_255, retro_ptro_842,
Pteropus vampyrus	ENSPVAG00000015560	5 retrocopies	retro_pvam_1197, retro_pvam_1261, retro_pvam_479, retro_pvam_512, retro_pvam_979,
Rattus norvegicus	ENSRNOG00000014224	1 retrocopy	retro_rnor_104,
Sarcophilus harrisii	ENSSHAG00000009016	2 retrocopies	retro_shar_167, retro_shar_207,
Sus scrofa	ENSSSCG00000003261	3 retrocopies	retro_sscr_45, retro_sscr_628, retro_sscr_97,
Ictidomys tridecemlineatus	ENSSTOG00000025377	2 retrocopies	retro_itri_1280, retro_itri_756,