RetrogeneDB ID: retro_ptro_1315

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:18327211..18327733(+)
• 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_1315
GTCCCGATCATCCATGGCCCAGGGAATAATGGAGAAGGTAGCCTGCTCTGTGCTTGACACCCCAAACATTTTGGTCACCA
GCCAATCATCTTTGACCCCAAAAGACCCAACAGGCCACTCTACACTATGCTGGTGACCCACCGTCAGGAAAGGGGCATTC
TTTTGCTTGGTGAAGTGCCCCCAGAGCCCACGCTGATCAATGAGCTGTATGAGCTGGGGGTGGATGCCATCTTTGGCTTC
AGCTTCAAGGGCAATGTTTGCAAGCCATTCTGTAACATTCTGAGTGTCCTGAATAGACTCACTGTGCCACTGCCAATGCT
GACATTCCCTTGGGATGGGACATGGAGAAGGAAAACTCCGGAGGGATCCAGCCAGACCTGCTTCTCTCCCTGATAGCACC
CCAAAAGTCTGAAACCTAGTTTACAGATTGCTACCACTACTTGAGGGGTTGTTGACTACCACCTGCTTGGGAAAAGAAGT
ACCAGCTAAAACCTGCCATTGTACCCTAACCCTGAGTATGTC

Alignment

ORF - retro_ptro_1315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.2 %
• Parental protein coverage: 60.42 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLVICGPGNNGGDGLVCARHLKLFGYEPTIYYPKRPNKPLFTALVTQCQKMDIPFLGEMPAEPMTIDELY
          V..I.GPGNNG...L.CA.H.K.FG..P.I..PKRPN.PL.T.LVT..Q...I..LGE.P.EP..I.ELY
Retrocopy VPIIHGPGNNGEGSLLCA*HPKHFGHQPIIFDPKRPNRPLYTMLVTHRQERGILLLGEVPPEPTLINELY

Parental  ELVVDAIFGFSFKGDVREPFHSILSVLKGLTVPI-ASIDIPSGWDVEKGNAGGIQPDLLISLTAPKKSAT
          EL.VDAIFGFSFKG.V..PF..ILSVL..LTVP..A..DIP.GWD.EK.N.GGIQPDLL.SL.AP.KS.T
Retrocopy ELGVDAIFGFSFKGNVCKPFCNILSVLNRLTVPL<ANADIPLGWDMEKENSGGIQPDLLLSLIAPQKSET

Parental  QFTGRYHYLGGRFVPPALEKKYQL-NLPPYPDTECV
          .FT..YHYL.G...PPA.EKKYQL.NLP.YP..E.V
Retrocopy *FTDCYHYLRGC*LPPAWEKKYQL>NLPLYPNPEYV

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	46.04 RPM
SRP007412_cerebellum	0.04 RPM	38.21 RPM
SRP007412_heart	0.00 RPM	51.85 RPM
SRP007412_kidney	0.00 RPM	82.93 RPM
SRP007412_liver	0.03 RPM	47.50 RPM
SRP007412_testis	0.00 RPM	34.04 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1315 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1315 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1315 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1973

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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,