RetrogeneDB ID: retro_mdom_830

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:131220549..131220797(-)
• Located in intron of: ENSMODG00000004644

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX5A
• Ensembl ID: ENSMODG00000028168
• Aliases: None
• Description: cytochrome c oxidase subunit Va [Source:HGNC Symbol;Acc:2267]

Sequence

>retro_mdom_830
TATTACTACAAACCAGATCTGGATGCCTAGAATTCCAAAAAGGAGTTAAAACACTGGTTGGCTATGACCTAGTTCCAGAA
CTTAAAATCATTGATACTGCTTCAAGGGCATGCAGACAGTCAGATGATTCTACTAGTAGAGTTTCCATTCTAGAAGCAGA
AGCAGGACCTCTTGAAGAAGTCTACTCATGTGTTATTAAGGAATTTAGACCAACTTTCAATAAACTGGAATCAGGAAAGG
CAGAGGAA

Alignment

ORF - retro_mdom_830 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.32 %
• Parental protein coverage: 65.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YFSKPDLDA-WELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVI
          Y..KPDLDA..E..KG..TLVGYDLVPE.KIID.A.RACR...D..S.V.ILE.....AGP..E.Y..VI
Retrocopy YYYKPDLDA<LEFQKGVKTLVGYDLVPELKIIDTASRACRQSDDSTSRVSILEA---EAGPLEEVYSCVI

Parental  QELRPTLDELGISTPEE
          .E.RPT...L.....EE
Retrocopy KEFRPTFNKLESGKAEE

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	387.15 RPM
SRP007412_cerebellum	0.00 RPM	497.19 RPM
SRP007412_heart	0.00 RPM	1659.21 RPM
SRP007412_kidney	0.00 RPM	936.27 RPM
SRP007412_liver	0.00 RPM	633.39 RPM
SRP007412_testis	0.00 RPM	478.71 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_830 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_830 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008643	2 retrocopies	retro_amel_546, retro_amel_706,
Bos taurus	ENSBTAG00000017267	1 retrocopy	retro_btau_711,
Canis familiaris	ENSCAFG00000017977	1 retrocopy	retro_cfam_29,
Choloepus hoffmanni	ENSCHOG00000006108	4 retrocopies	retro_chof_1291, retro_chof_1434, retro_chof_2330, retro_chof_695,
Callithrix jacchus	ENSCJAG00000015613	6 retrocopies	retro_cjac_2567, retro_cjac_3167, retro_cjac_3229, retro_cjac_703, retro_cjac_9, retro_cjac_982,
Cavia porcellus	ENSCPOG00000024832	3 retrocopies	retro_cpor_1248, retro_cpor_770, retro_cpor_970,
Felis catus	ENSFCAG00000010587	3 retrocopies	retro_fcat_1100, retro_fcat_1201, retro_fcat_253,
Homo sapiens	ENSG00000178741	3 retrocopies	retro_hsap_1036, retro_hsap_1337, retro_hsap_1416,
Gorilla gorilla	ENSGGOG00000024426	3 retrocopies	retro_ggor_1041, retro_ggor_1096, retro_ggor_817,
Loxodonta africana	ENSLAFG00000006266	1 retrocopy	retro_lafr_1192,
Macropus eugenii	ENSMEUG00000013942	2 retrocopies	retro_meug_1280, retro_meug_784,
Myotis lucifugus	ENSMLUG00000013702	1 retrocopy	retro_mluc_337,
Macaca mulatta	ENSMMUG00000011677	2 retrocopies	retro_mmul_2176, retro_mmul_2255,
Monodelphis domestica	ENSMODG00000028168	1 retrocopy	retro_mdom_830 ,
Mustela putorius furo	ENSMPUG00000017314	1 retrocopy	retro_mputfur_652,
Mus musculus	ENSMUSG00000000088	2 retrocopies	retro_mmus_1413, retro_mmus_742,
Nomascus leucogenys	ENSNLEG00000014708	4 retrocopies	retro_nleu_1821, retro_nleu_1838, retro_nleu_2647, retro_nleu_909,
Otolemur garnettii	ENSOGAG00000005611	5 retrocopies	retro_ogar_1540, retro_ogar_2150, retro_ogar_2432, retro_ogar_2585, retro_ogar_604,
Pongo abelii	ENSPPYG00000006652	1 retrocopy	retro_pabe_197,
Pan troglodytes	ENSPTRG00000007289	3 retrocopies	retro_ptro_706, retro_ptro_914, retro_ptro_969,
Pteropus vampyrus	ENSPVAG00000012957	1 retrocopy	retro_pvam_438,
Rattus norvegicus	ENSRNOG00000018816	1 retrocopy	retro_rnor_1867,
Sarcophilus harrisii	ENSSHAG00000015941	2 retrocopies	retro_shar_238, retro_shar_422,
Tursiops truncatus	ENSTTRG00000008004	2 retrocopies	retro_ttru_161, retro_ttru_765,