RetrogeneDB ID: retro_ptro_2215

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:179273172..179274021(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOA1BP
• Ensembl ID: ENSPTRG00000001463
• Aliases: None
• Description: NAD(P)H-hydrate epimerase [Source:UniProtKB/TrEMBL;Acc:H2Q098]

Sequence

>retro_ptro_2215
ATGTCCGGCCTGCGGGCGCTGCCGGGCTCGGGCTGCTGGCTGCGGCTCGCGCCTGCGCGAATCAAAAGCCAGACCAGCGC
CTGCCGCTCGGGACCCACCTAGTGGGGACCGCAGCGGCTGAACTCGGGTGGCCGCTGGGACTCAGCGGTCATGGCGAGCA
TAGCGGTGAAGCACCTGAGCCAGGAGGAAGCCCAGGCCGTGGACCAGGAGCTATTCAACGAGTACTAGTTCAGCGTGGAC
CGACTTGTGGAGCTGGCCGGGCTGAGCTGTGCCGCAGCCATCGCCGAGGCATATTCCCCCACGTCCATGTCCAGGAGCTC
CACTACTGTCCTGGTCATCTGTGGCCCGGGGAATAATGGAGGAGATGGTCTGGTCTGTGCTCCGCACCTCAAACTCTTTG
GCTAACCAGCCAACCCTCTATTACCCCAAAAGGCCTAACAAGCCCCTCTTCATTGCGTTGGTGACCCCGCGTCAGAAAAT
GGACATCCCTTTCCTTGGGGAAATGCGCTCAGAGCCCGTGATGATTGAGCTGTATGAGCTGGTGGTGGATGCCATCTTCG
GCTTCAGCTTCGAGGGTGATGTTCGGGAACGTTCCACAGCATCCTGAGGGTCCTGAAGGGATTCACCGTGCCCACTGCCG
GCATCAACATTCCCTCAGGATGGGATGTGGAGAAGGGAAACTCTGGAGGGATCCAGCCAGACTTGCTCATCTCCCTCACA
GCACCCAAAAAGTCTGCAACCCAGGTTACCCGGTCGCCACCATTACCTGGGGGGTCGTTTTGTGCCACCTGCTCTGGAAA
AGAAGTAGCAGCTGAACCTGCCCCCTACCCTGACACCAAGTGTGTGTAT

Alignment

ORF - retro_ptro_2215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.22 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MSRLRAL-LGLGLLVA-GSRL-PRIKSQTVACRSGPTWWGPQRLNSGGRWDSEVMASTVVKYLSQEEAQA
          MS.LRAL..GLGLL.A.GSRL..RIKSQT.ACRSGPT.WGPQRLNSGGRWDS.VMAS..VK.LSQEEAQA
Retrocopy MSGLRAL<AGLGLLAA<GSRL<ARIKSQTSACRSGPT*WGPQRLNSGGRWDSAVMASIAVKHLSQEEAQA

Parental  VDQELFNEYQFSVDQLMELAGLSCATAIAKAYPPTSMSRSPPTVLVICGPGNNGGDGLVCARHLKLFG-Y
          VDQELFNEY.FSVD.L.ELAGLSCA.AIA.AY.PTSMSRS..TVLVICGPGNNGGDGLVCA.HLKLFG..
Retrocopy VDQELFNEY*FSVDRLVELAGLSCAAAIAEAYSPTSMSRSSTTVLVICGPGNNGGDGLVCAPHLKLFG>N

Parental  EPTIYYPKRPNKPLFTALVTQCQKMDIPFLGEMPAEPMTIDELYELVVDAIFGFSFKGDVRE-PFHSILS
          .PT.YYPKRPNKPLF.ALVT..QKMDIPFLGEM..EP..I.ELYELVVDAIFGFSF.GDVRE..FHSIL.
Retrocopy QPTLYYPKRPNKPLFIALVTPRQKMDIPFLGEMRSEPVMI-ELYELVVDAIFGFSFEGDVRE<TFHSILR

Parental  VLKGLTVPIASIDIPSGWDVEKGNAGGIQPDLLISLTAPKKSATQFT-GRYHYLGGRFVPPALEKKYQLN
          VLKG.TVP.A.I.IPSGWDVEKGN.GGIQPDLLISLTAPKKSATQ.T.GR.HYLGGRFVPPALEKK.QLN
Retrocopy VLKGFTVPTAGINIPSGWDVEKGNSGGIQPDLLISLTAPKKSATQVT>GRHHYLGGRFVPPALEKK*QLN

Parental  LP-PYPDTECVY
          LP.PYPDT.CVY
Retrocopy LP<PYPDTKCVY

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	0.09 RPM	46.04 RPM
SRP007412_cerebellum	0.00 RPM	38.21 RPM
SRP007412_heart	0.00 RPM	51.85 RPM
SRP007412_kidney	0.03 RPM	82.93 RPM
SRP007412_liver	0.10 RPM	47.50 RPM
SRP007412_testis	0.21 RPM	34.04 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2215 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2215 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2215 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3275
Gorilla gorilla	retro_ggor_2228
Pongo abelii	retro_pabe_2709
Macaca mulatta	retro_mmul_2060

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000163382	2 retrocopies	retro_hsap_1973, retro_hsap_3275,
Gorilla gorilla	ENSGGOG00000000754	1 retrocopy	retro_ggor_2228,
Macaca mulatta	ENSMMUG00000002623	2 retrocopies	retro_mmul_1364, retro_mmul_2060,
Nomascus leucogenys	ENSNLEG00000012663	2 retrocopies	retro_nleu_2615, retro_nleu_2992,
Pongo abelii	ENSPPYG00000000713	2 retrocopies	retro_pabe_1692, retro_pabe_2709,
Pan troglodytes	ENSPTRG00000001463	2 retrocopies	retro_ptro_1315, retro_ptro_2215 ,