RetrogeneDB ID: retro_mdom_327

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:148500480..148501349(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000011078
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UQCRC2
• Ensembl ID: ENSMODG00000007645
• Aliases: None
• Description: ubiquinol-cytochrome c reductase core protein II [Source:HGNC Symbol;Acc:12586]

Sequence

>retro_mdom_327
GAAAACTATGCTCCAGCTTCAAGAATTGGTTTATTCATTAAAGCTGGTAGTAGATATGAAGATGCTACCAATTTTGGAAC
CTCCCATTTACTCTGTCTTGCATCTAATTTGACTACCAAAAGAGCTTCTTCTTTTAAGATAACTCGAGGGACTGAAGCAG
TTGGTGGCAAATTAAGTGTGACTGGTACAAGGGAAAATATGGCTTATACAGCAGATTACCTTCATGATGATATTGATATT
CTAATGGAGTTCCTGCTCAATGTCACCACAGCACCAGAATTTCGACACTGGGAAGTAGCAGATCTTCAGTCACAGCTAAA
GATTGATAAAGAAATTGCTTTTCAAAACCCCGAAACTGGTGTGATTGAAAATCTGCATGTTGTAACTTATTGGAATGCTC
TTTCAAATTCCTTGTATTGTCCTGATTATAAGGTTGGAAAAATTACTCCAGAAGAGCTTCATTATTATATACAGAACAAT
TTTACAAGTGCAAGAATGGCTCTGGTTGGAATTGGTGTAGGCCATACTATCCCGAAGCAAGTTGCTAAGCAGTTTCTAAA
TATGAGGGGTGGGCCTGGCATGTCTGGTGCAAAGGCACAATACAATGGAGGTGAAATTCGAGTGCAGAATGGTGATAGTC
TTGTCCATGCTGCATTGTAGCTGAGGGAGCTACCTCAGGAAGTGCAGAGGCAAATGCATTTAGTATCCTTCAGCATGTCC
TTGGAGCAGGCCCTCATGTTAAGAGGGGTAGCAATGTTACCAGCCTGCTATGCCAGGCTGTGGCCAAGGGAACAAACCAG
CCATTTGATGTTTCAGCCTTTAATGCAAATTACTCTGATTCTAGACTCTGGGATTTATGCTATATCTCA

Alignment

ORF - retro_mdom_327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.41 %
• Parental protein coverage: 63.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ENYAPASRIGLFIKAGSRYEDATNFGTSHLLRLASNLTTKGASSFKITRGTEAVGGKLSVTGTRENMAYT
          ENYAPASRIGLFIKAGSRYEDATNFGTSHLL.LASNLTTK.ASSFKITRGTEAVGGKLSVTGTRENMAYT
Retrocopy ENYAPASRIGLFIKAGSRYEDATNFGTSHLLCLASNLTTKRASSFKITRGTEAVGGKLSVTGTRENMAYT

Parental  ADCLRDDIDILMEYLLNVTTAPEFRRWEVADLQSQLKIDKEVAFQNPQTGVIENLHAVAYRNALSNPLYC
          AD.L.DDIDILME.LLNVTTAPEFR.WEVADLQSQLKIDKE.AFQNP.TGVIENLH.V.Y.NALSN.LYC
Retrocopy ADYLHDDIDILMEFLLNVTTAPEFRHWEVADLQSQLKIDKEIAFQNPETGVIENLHVVTYWNALSNSLYC

Parental  PDYKIGKITPEELHYYIQNNFTSARMALVGIGVDHTILKQVAEQFLNMRGGLGMSGAKAQYYGGEIRVQN
          PDYK.GKITPEELHYYIQNNFTSARMALVGIGV.HTI.KQVA.QFLNMRGG.GMSGAKAQY.GGEIRVQN
Retrocopy PDYKVGKITPEELHYYIQNNFTSARMALVGIGVGHTIPKQVAKQFLNMRGGPGMSGAKAQYNGGEIRVQN

Parental  GDSLVHAA-IVAEGATSGSAEANAFSILQHVLGAGPHVKRGSNVTSLLCQAVAKGTNQPFDVSAFNANYS
          GDSLVHAA.IVAEGATSGSAEANAFSILQHVLGAGPHVKRGSNVTSLLCQAVAKGTNQPFDVSAFNANYS
Retrocopy GDSLVHAA<IVAEGATSGSAEANAFSILQHVLGAGPHVKRGSNVTSLLCQAVAKGTNQPFDVSAFNANYS

Parental  DSGLFGIYAIS
          DS.L.....IS
Retrocopy DSRLWDLCYIS

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	0.48 RPM	0.00 RPM
SRP007412_cerebellum	0.33 RPM	0.00 RPM
SRP007412_heart	0.40 RPM	0.00 RPM
SRP007412_kidney	1.32 RPM	0.00 RPM
SRP007412_liver	0.50 RPM	0.00 RPM
SRP007412_testis	0.39 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_327 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_327 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 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021651	2 retrocopies	retro_btau_1008, retro_btau_1668,
Canis familiaris	ENSCAFG00000017756	1 retrocopy	retro_cfam_2075,
Callithrix jacchus	ENSCJAG00000009116	1 retrocopy	retro_cjac_222,
Echinops telfairi	ENSETEG00000001084	1 retrocopy	retro_etel_2087,
Homo sapiens	ENSG00000140740	1 retrocopy	retro_hsap_2785,
Gorilla gorilla	ENSGGOG00000015379	1 retrocopy	retro_ggor_1941,
Myotis lucifugus	ENSMLUG00000003345	2 retrocopies	retro_mluc_1391, retro_mluc_770,
Macaca mulatta	ENSMMUG00000018287	2 retrocopies	retro_mmul_1442, retro_mmul_683,
Monodelphis domestica	ENSMODG00000007645	1 retrocopy	retro_mdom_327 ,
Mustela putorius furo	ENSMPUG00000016849	1 retrocopy	retro_mputfur_1042,
Nomascus leucogenys	ENSNLEG00000012185	1 retrocopy	retro_nleu_685,
Oryctolagus cuniculus	ENSOCUG00000003891	2 retrocopies	retro_ocun_604, retro_ocun_739,
Otolemur garnettii	ENSOGAG00000005478	4 retrocopies	retro_ogar_1113, retro_ogar_112, retro_ogar_1934, retro_ogar_82,
Ochotona princeps	ENSOPRG00000000419	1 retrocopy	retro_opri_455,
Pongo abelii	ENSPPYG00000007174	1 retrocopy	retro_pabe_2232,
Pan troglodytes	ENSPTRG00000007871	1 retrocopy	retro_ptro_1886,
Sorex araneus	ENSSARG00000010670	1 retrocopy	retro_sara_231,
Tupaia belangeri	ENSTBEG00000010785	1 retrocopy	retro_tbel_3988,
Vicugna pacos	ENSVPAG00000010914	1 retrocopy	retro_vpac_640,