RetrogeneDB ID: retro_pabe_993

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:42938812..42939386(+)
• Located in intron of: ENSPPYG00000005322

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC4
• Ensembl ID: ENSPPYG00000017352
• Aliases: None
• Description: zinc finger, DHHC-type containing 4 [Source:HGNC Symbol;Acc:18471]

Sequence

>retro_pabe_993
CATACCTTCATTATCCTCCACCTGGTCTTGCAAGGGATGGTAAATACCGAATATACCTGGGAAATACTTGGCTACCGTCA
AAAGCTAGTTCTCCTGTATTACCTTCTTCTGCCCTATCTGCTTCTGATTGTAAACCCGTTTATTTCCACCCTAACTTGTG
TAACTGATTCTGGCATTATAAGAAAAGCAAATGAATTATTTCTTCAAGTTTATGAATTCAATGAAGTGATGTTTCTAAAG
AGGTGAGGTGCTCTACTTATGACTGATGAGCACCAGCTCGATCTAAGCACTGACTGCAGTGTGCGCGCCATTTTGACCAT
CTTGGGTTTGGGTGAACAACTGCATCTGGGCTTGGAACACCAGTTATTAATACTTTCTCAGCTACCTCTTGATGTTGATG
GCCTCGGCTGCTGCGATGGCCATTGTGAGCACTGCGTTTCTGGTCGACTTGGTGGTATTGTTGGATTCATACTAGACTTA
CACTGATGACCTTGGACACTTCCAGTTTATGGACTTGATTTTTCTTATTCAGTACCTGTTCCTGACCTTTCCAACAATTG
TTTTCATGCTGGGG

Alignment

ORF - retro_pabe_993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.5 %
• Parental protein coverage: 56.98 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HTFIVLHLVLQGMVYTEYTWEVFGYCQELDFSLYYLLLPYLLLVVNLFSFTLTCVTNPGVITKANELLFL
          HTFI.LHLVLQGMV.TEYTWE..GY.Q.L...LYYLLLPYLLL.VN.F..TLTCVT..G.I.KANE.LFL
Retrocopy HTFIILHLVLQGMVNTEYTWEILGYRQKL-VLLYYLLLPYLLLIVNPFISTLTCVTDSGIIRKANE-LFL

Parental  HVYEFDELMF-PKNVRCSTCDLRKPARSKHCSVCNWCVHRFDH-HCVWVNNCIGAWNIR--YFLIYLLTL
          .VYEF.E.MF..K.VRCST.D...PARSKH...C......FDH...VWVNNCI.AWN....YFL.YLL.L
Retrocopy QVYEFNEVMF<SKEVRCSTYD**APARSKH*LQC---ARHFDH<SWVWVNNCIWAWNTSY*YFLSYLLML

Parental  TASAATVAIVSTTFLVHLVVMSDLYQETYTDDLGHLHVMDTVFLIQYLFLTFPRIVFMLG
          .ASAA..AIVST.FLV.LVV..D.Y..TYTDDLGH...MD..FLIQYLFLTFP.IVFMLG
Retrocopy MASAAAMAIVSTAFLVDLVVLLDSY-*TYTDDLGHFQFMDLIFLIQYLFLTFPTIVFMLG

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	0.17 RPM	6.58 RPM
SRP007412_cerebellum	0.00 RPM	5.72 RPM
SRP007412_heart	0.09 RPM	5.30 RPM
SRP007412_kidney	0.20 RPM	13.66 RPM
SRP007412_liver	0.15 RPM	12.82 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_993 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_993 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_993 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1193
Pan troglodytes	retro_ptro_3038
Macaca mulatta	retro_mmul_1283

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009547	1 retrocopy	retro_btau_643,
Dasypus novemcinctus	ENSDNOG00000009165	1 retrocopy	retro_dnov_2610,
Homo sapiens	ENSG00000136247	1 retrocopy	retro_hsap_1193,
Macaca mulatta	ENSMMUG00000015545	1 retrocopy	retro_mmul_1283,
Nomascus leucogenys	ENSNLEG00000015607	1 retrocopy	retro_nleu_2081,
Pongo abelii	ENSPPYG00000017352	1 retrocopy	retro_pabe_993 ,
Pan troglodytes	ENSPTRG00000018915	1 retrocopy	retro_ptro_3038,
Pteropus vampyrus	ENSPVAG00000016104	2 retrocopies	retro_pvam_1175, retro_pvam_758,
Ictidomys tridecemlineatus	ENSSTOG00000011605	1 retrocopy	retro_itri_1054,
Tursiops truncatus	ENSTTRG00000005001	1 retrocopy	retro_ttru_179,
Vicugna pacos	ENSVPAG00000011480	1 retrocopy	retro_vpac_177,