RetrogeneDB ID: retro_pabe_2668

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:98461841..98462442(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC3
• Ensembl ID: ENSPPYG00000013950
• Aliases: None
• Description: zinc finger, DHHC-type containing 3 [Source:HGNC Symbol;Acc:18470]

Sequence

>retro_pabe_2668
ATGATGCTGGTCCCCGCCCACCGCTTCAGAGACTTTGAGAGGAAAACAGAGTACCCATAGCTGGAGATGCCTGTCTGACC
TCCCTACCCTGGTCCCGTGAGAACCATGTGATTTATCCACAAGGGCTGTGGCATTGCCTATGCCATCATCACCTGGTTTC
TGGTCCTCTATGCAGAGTTTGTGGTCCTCTTTTTCATGCTGATTCCATCCTGAGACTATGCATACAGCACCATCAATGGA
ATTATGTTCAACCTGCTGACTTTCTTGGCCCTGGCCTCCCACTGCCAGGCCATGCTGACAGACACCAGAGCAGTGCTTAA
ATGAAATGCCACTAAATAATTCATCCCGAGTTTACAGATGAAGCCCAGGCATGTGGTGTACTCATGTCCCAGTGCTGCAG
GATCAAGCCTGACTGAGCCTGCCGCCACAGTGTTTGTAAGAGGTGCATTTGCAGGGTGGAACCCCACTGTCCCTGGGTCA
ACATCTGCATCGAAGAGAACAACCAGAATTGCTTTGTCCTGTTTATCATGTGCACAGCTCTCATTTCCTTACCTGCCCTC
ACTGTGGTGGATTCCACTTCCTGGATTGCTGTGAAGAAGAT

Alignment

ORF - retro_pabe_2668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.44 %
• Parental protein coverage: 61.47 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMLIPTHHFRDIERKPEYLQPEKCVPPPYPGPVGTMWFIRDGCGIACAIVTWFLVLYAEFVVLFVMLIPS
          MML.P.H.FRD.ERK.EY...E..V.PPYPGPV.TM.FI..GCGIA.AI.TWFLVLYAEFVVLF.MLIPS
Retrocopy MMLVPAHRFRDFERKTEYP*LEMPV*PPYPGPVRTM*FIHKGCGIAYAIITWFLVLYAEFVVLFFMLIPS

Parental  RDYVYSIINGIVFNLLAFLALASHCRAMLTDPGAVPKGNATKEFIESLQLKPGQVVYKCP-KCCSIKPDR
          .DY.YS.INGI.FNLL.FLALASHC.AMLTD..AV.K.NATK.FI.SLQ.KP..VVY.CP..CC.IKPD.
Retrocopy *DYAYSTINGIMFNLLTFLALASHCQAMLTDTRAVLK*NATK*FIPSLQMKPRHVVYSCP<QCCRIKPD*

Parental  AHHCSVCKRCIRKMDHHCPWVNNCVGENNQKYFVLFTMYIALISLHALIMV-GFHFLHCFEED
          A...SVCKRCI.....HCPWVN.C..ENNQ..FVLF.M..ALISL.AL..V.GFHFL.C.EED
Retrocopy ACRHSVCKRCICRVEPHCPWVNICIEENNQNCFVLFIMCTALISLPALTVV<GFHFLDCCEED

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	0.00 RPM	40.14 RPM
SRP007412_cerebellum	0.00 RPM	35.39 RPM
SRP007412_heart	0.00 RPM	14.69 RPM
SRP007412_kidney	0.00 RPM	26.58 RPM
SRP007412_liver	0.00 RPM	12.12 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2668 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2668 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2668 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3221
Pan troglodytes	retro_ptro_2171
Gorilla gorilla	retro_ggor_2187

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000163812	1 retrocopy	retro_hsap_3221,
Pongo abelii	ENSPPYG00000005201	1 retrocopy	retro_pabe_1081,
Pongo abelii	ENSPPYG00000013950	1 retrocopy	retro_pabe_2668 ,
Pan troglodytes	ENSPTRG00000014829	1 retrocopy	retro_ptro_2171,