RetrogeneDB ID: retro_mdom_1105

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:122238737..122239130(-)
• Located in intron of: ENSMODG00000003756

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB5
• Ensembl ID: ENSMODG00000021300
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa [Source:HGNC Symbol;Acc:7700]

Sequence

>retro_mdom_1105
GTTCTACATAGTGGAGGCCATGTGAAGAAAAATGTTTCTCATAACATATTATGGATTTTATGACAACAGAAGTTTGATGT
TGTTGAGATTTTATTTATTGTTTACTGGGATTCTAGTAGCAATTGGCATAACATTATTGAATATATTCATTGGCAAAGAT
GAATTAACAGAAATCACTGAAGGCTACATTCCATAAAACTAGGAAACTTTAAGTATCCTATAACCAGGTGGATTGCTTGT
TATGTCTATGAACCTTTTGAAAAGAATGATGAGAGAAAGATGACAATCCTTCAATTATAAGCTGAAAAGTTTGATCCAAT
GTTAAAGTTTTAGGAAACAAAAAGACTTATGTGATAAGTAGGATCCTGGTTTCATTACCCAACTATTGATAAG

Alignment

ORF - retro_mdom_1105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.96 %
• Parental protein coverage: 68.21 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VRHSGGHGKR-MFLIKASEFYDKRFLKLLRFYLLLTGIPVAVGITFVNIFIGEAELAEIPDGYVPEHWE-
          V.HSGGH.K..MFLI....FYD.R.L.LLRFYLL.TGI.VA.GIT..NIFIG..EL.EI..GY.P...E.
Retrocopy VLHSGGHVKK>MFLITYYGFYDNRSLMLLRFYLLFTGILVAIGITLLNIFIGKDELTEITEGYIP*N*E<

Parental  YYKHPITRWIARYVYEPPEKNYERTMAILQVEAEKADLRLKLQATDRLMRERGDGPWFHYPTVDK
          ..K.PITRWIA.YVYEP.EKN.ER.M.ILQ..AEK.D..LK...T.RLM...G...WFHYPT.DK
Retrocopy NFKYPITRWIACYVYEPFEKNDERKMTILQL*AEKFDPMLKF*ETKRLM**VGS--WFHYPTIDK

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1105 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1105 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 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002684	1 retrocopy	retro_chof_1511,
Equus caballus	ENSECAG00000000682	1 retrocopy	retro_ecab_235,
Echinops telfairi	ENSETEG00000019363	1 retrocopy	retro_etel_1110,
Homo sapiens	ENSG00000136521	2 retrocopies	retro_hsap_3127, retro_hsap_4879,
Macropus eugenii	ENSMEUG00000014166	1 retrocopy	retro_meug_1852,
Myotis lucifugus	ENSMLUG00000000999	1 retrocopy	retro_mluc_2181,
Macaca mulatta	ENSMMUG00000009746	1 retrocopy	retro_mmul_2619,
Monodelphis domestica	ENSMODG00000021300	1 retrocopy	retro_mdom_1105 ,
Nomascus leucogenys	ENSNLEG00000005842	2 retrocopies	retro_nleu_2247, retro_nleu_2558,
Pongo abelii	ENSPPYG00000014493	2 retrocopies	retro_pabe_3018, retro_pabe_3796,
Pan troglodytes	ENSPTRG00000015649	1 retrocopy	retro_ptro_3252,
Pteropus vampyrus	ENSPVAG00000004286	1 retrocopy	retro_pvam_81,
Sorex araneus	ENSSARG00000006918	1 retrocopy	retro_sara_200,
Sus scrofa	ENSSSCG00000011764	1 retrocopy	retro_sscr_193,
Ictidomys tridecemlineatus	ENSSTOG00000010557	1 retrocopy	retro_itri_1810,
Tursiops truncatus	ENSTTRG00000008910	3 retrocopies	retro_ttru_1445, retro_ttru_1719, retro_ttru_1755,