RetrogeneDB ID: retro_hsap_3127

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:181494669..181494975(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000251025
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDUFB5
• Ensembl ID: ENSG00000136521
• Aliases: NDUFB5, CISGDH, SGDH
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa [Source:HGNC Symbol;Acc:7700]

Sequence

>retro_hsap_3127
TTATTGAAATTCCACATTTTGTTGACTGGGATTCCAGCAGCAGCTTGCATAACTTTGGTGAATGGATGCATGGGTGAAGC
TGAACTAGCAGAAAGTCCAAAAGCCTATATCCCAGAACATTGGGAATACTATAAGCATCCTATATCAAGACGGATTGCCC
ACAGTTTCCATAATAGTCCTGAAAAGAACTATGAAAGAGCAGTGACCGTCATTCAGATCGAAGCCAAAAAGGCTGAATTA
CAGTTAAAGCAGCTGGAAATATGAAGATTAATACCTGACAGAGGAGATGGGCCCTAGTATGAATAT

Alignment

ORF - retro_hsap_3127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.71 %
• Parental protein coverage: 53.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLRFYIALTGIPVAIFITLVNVFIGQAELAEIPEGYVPEHWEYYKHPISRWIARNFYDSPEKIYERTMAV
          LL.F.I.LTGIP.A..ITLVN...G.AELAE.P..Y.PEHWEYYKHPISR.IA..F..SPEK.YER...V
Retrocopy LLKFHILLTGIPAAACITLVNGCMGEAELAESPKAYIPEHWEYYKHPISRRIAHSFHNSPEKNYERAVTV

Parental  LQIEAEKAELRVKELEVRKLMHVRGDGPWYYY
          .QIEA.KAEL..K.LE...L...RGDGP.Y.Y
Retrocopy IQIEAKKAELQLKQLEI*RLIPDRGDGP*YEY

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
bodymap2_adipose	0.00 RPM	48.58 RPM
bodymap2_adrenal	0.00 RPM	35.56 RPM
bodymap2_brain	0.00 RPM	94.86 RPM
bodymap2_breast	0.00 RPM	105.64 RPM
bodymap2_colon	0.00 RPM	83.78 RPM
bodymap2_heart	0.00 RPM	142.67 RPM
bodymap2_kidney	0.00 RPM	103.42 RPM
bodymap2_liver	0.00 RPM	48.08 RPM
bodymap2_lung	0.00 RPM	37.94 RPM
bodymap2_lymph_node	0.00 RPM	50.44 RPM
bodymap2_ovary	0.04 RPM	48.21 RPM
bodymap2_prostate	0.00 RPM	76.75 RPM
bodymap2_skeletal_muscle	0.00 RPM	66.66 RPM
bodymap2_testis	0.00 RPM	80.28 RPM
bodymap2_thyroid	0.00 RPM	69.17 RPM
bodymap2_white_blood_cells	0.00 RPM	56.48 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3127 was not detected

EST

No EST(s) were mapped for retro_hsap_3127 retrocopy.

TSS

No TSS is located nearby retro_hsap_3127 retrocopy 5' end.

Lab

retro_hsap_3127 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3127 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 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,
Tursiops truncatus	ENSTTRG00000008910	3 retrocopies	retro_ttru_1445, retro_ttru_1719, retro_ttru_1755,