RetrogeneDB ID: retro_ptro_1012

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:44002544..44002990(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYB5B
• Ensembl ID: ENSPTRG00000008282
• Aliases: None
• Description: Pan troglodytes cytochrome b5 type B (CYB5B), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001242609]

Sequence

>retro_ptro_1012
ATTTCCAGTCCAATGGCAACTGTGCAAGCTAGCAGCAGTGATGAAAAAGGGCAGGGGGTAGGGACTTCCACCACCTATTA
GCAGTTGGAGGAGGTGGTGAAGCAAAACTTCCTGAAGGAACTGTGTCTAGTAATCCATGGGCGACTCTACGATGTTCCCC
ACTTTGAGGATCCCCCTGGCAGAGAAAAGGTTCTGCTGGAACAAGCTGGTGCAGATGCAACTGAAAGTTTTGTAGATGTA
GGCCACTCCTCTGATGCCAGAGAAATGCTAAAGCAGTACTATATTGGTGCTGTCCATTTGAGTGACCTCAAACCTGAAAA
TTGTGCAAGGATTCTTCAAAAAATGACACATGCAAAAGTTTCTGGCCATATTGGATTTTCCCTATCATAGGTGCTATCCT
CTTAGGTTACCTGTCTCACTCCTACATATTGGAAAGCAAATCCTCC

Alignment

ORF - retro_ptro_1012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGSMATAEASGSDGKGQEVETSVTYYRLEEVAKRNSLKELWLVIHGRVYDVTRFLNEHPGGEEVLLEQA
          .S..MAT..AS.SD.KGQ.V.TS.TY..LEEV.K.N.LKEL.LVIHGR.YDV..F....PG.E.VLLEQA
Retrocopy ISSPMATVQASSSDEKGQGVGTSTTY*QLEEVVKQNFLKELCLVIHGRLYDVPHF-EDPPGREKVLLEQA

Parental  GVDASESFEDVGHSSDAREMLKQYYIGDIHPSDLKPESGS-KDPSKNDTCKSCWAYWILPIIGAVLLGFL
          G.DA.ESF.DVGHSSDAREMLKQYYIG..H.SDLKPE....KD.SKNDTCKS.W.YWI.PIIGA.LLG.L
Retrocopy GADATESFVDVGHSSDAREMLKQYYIGAVHLSDLKPENCA<KDSSKNDTCKSFWPYWIFPIIGAILLGYL

Parental  YRYYTSESKSS
          ...Y..ESKSS
Retrocopy SHSYILESKSS

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_prefrontal_cortex	0.02 RPM	53.41 RPM
SRP007412_cerebellum	0.00 RPM	32.19 RPM
SRP007412_heart	0.00 RPM	31.89 RPM
SRP007412_kidney	0.05 RPM	50.63 RPM
SRP007412_liver	0.00 RPM	39.38 RPM
SRP007412_testis	0.11 RPM	40.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1012 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1012 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1012 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1493
Gorilla gorilla	retro_ggor_1146
Pongo abelii	retro_pabe_1243
Macaca mulatta	retro_mmul_128

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000007518	1 retrocopy	retro_apla_13,
Dasypus novemcinctus	ENSDNOG00000008313	9 retrocopies	retro_dnov_1424, retro_dnov_2077, retro_dnov_2123, retro_dnov_2310, retro_dnov_2684, retro_dnov_2685, retro_dnov_706, retro_dnov_716, retro_dnov_728,
Felis catus	ENSFCAG00000024541	1 retrocopy	retro_fcat_1816,
Homo sapiens	ENSG00000103018	1 retrocopy	retro_hsap_1493,
Gallus gallus	ENSGALG00000000660	1 retrocopy	retro_ggal_13,
Gorilla gorilla	ENSGGOG00000015031	1 retrocopy	retro_ggor_1146,
Meleagris gallopavo	ENSMGAG00000008619	1 retrocopy	retro_mgal_12,
Myotis lucifugus	ENSMLUG00000006608	1 retrocopy	retro_mluc_1734,
Macaca mulatta	ENSMMUG00000012039	1 retrocopy	retro_mmul_128,
Nomascus leucogenys	ENSNLEG00000005515	1 retrocopy	retro_nleu_1715,
Oryctolagus cuniculus	ENSOCUG00000007729	2 retrocopies	retro_ocun_141, retro_ocun_255,
Pongo abelii	ENSPPYG00000007506	1 retrocopy	retro_pabe_1243,
Pan troglodytes	ENSPTRG00000008282	1 retrocopy	retro_ptro_1012 ,
Pan troglodytes	ENSPTRG00000010111	3 retrocopies	retro_ptro_1421, retro_ptro_898, retro_ptro_943,
Pteropus vampyrus	ENSPVAG00000015984	1 retrocopy	retro_pvam_977,
Sarcophilus harrisii	ENSSHAG00000014200	1 retrocopy	retro_shar_688,
Tarsius syrichta	ENSTSYG00000014292	1 retrocopy	retro_tsyr_2171,
Tursiops truncatus	ENSTTRG00000010016	1 retrocopy	retro_ttru_521,
Drosophila melanogaster	FBgn0029854	1 retrocopy	retro_dmel_39,