RetrogeneDB ID: retro_hsap_4683

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:51453835..51454390(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000223591
• Aliases: CENPVP1, CENPVL1, PRR6L1
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CENPV
• Ensembl ID: ENSG00000166582
• Aliases: CENPV, 3110013H01Rik, CENP-V, PRR6, p30
• Description: centromere protein V [Source:HGNC Symbol;Acc:29920]

Sequence

>retro_hsap_4683
CCCTCCGCGCCAACCCCGGACCCGCCGGGGCCCGCCCCGTCCCCCAAGGATCTGGACCTGGGCGCACAGCGGGAGCGCTG
GGAGACGTTCAGGAAGCTGCGGGGCCTCAGCTGCGAGGGCGCCGCCAAGGTCCTGCTGGACACCTTCGAGTACCCGGGCC
TCGTGCATCACACCGGGGGCTGCCACTGCGGCGCGGTCCGCTTTGCGGTCTGGGCCCCTGCAGATCTGCGCGTCGTGGAT
TGCAGCTGCAGGCTGTGCAGGAAGAAGCAGCACCGCCACTTCCTCGTCCCGGCCTCGCGCTTCACGCTGCTCCAGGGCGC
AGAAAGCATCGTCACCTATCGGTCCAACACGCACCCGGCGCTGCACAGCTTCTGCAGCAGGTGCGGGGTGCAGAGTTTCC
ACGCAGCTGTCTCTGACCCCCGCGTGTACGGCGTCGCCCCGCACTGCCTGGACGAGGGCACCGTGCGCAGCGTGGTCATC
GAGGAGGTCGGCGGTGGCGACCCGGGGGAGGAGGCCGCCGAGGAGCACAAGGCCATCCACAAGACGTCCTCCCAG

Alignment

ORF - retro_hsap_4683 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.78 %
• Parental protein coverage: 67.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPPPPPTPATPTSSASNLDLGEQRERWETFQKRQKLTSEGAAKLLLDTFEYQGLVKHTGGCHCGAVRFEV
          P..P.P.P..P..S...LDLG.QRERWETF.K...L..EGAAK.LLDTFEY.GLV.HTGGCHCGAVRF.V
Retrocopy PSAPTPDPPGPAPSPKDLDLGAQRERWETFRKLRGLSCEGAAKVLLDTFEYPGLVHHTGGCHCGAVRFAV

Parental  WASADLHIFDCNCSICKKKQNRHFIVPASRFKLLKGAEHITTYTFNTHKAQHTFCKRCGVQSFYTPRSNP
          WA.ADL...DC.C..C.KKQ.RHF.VPASRF.LL.GAE.I.TY..NTH.A.H.FC.RCGVQSF....S.P
Retrocopy WAPADLRVVDCSCRLCRKKQHRHFLVPASRFTLLQGAESIVTYRSNTHPALHSFCSRCGVQSFHAAVSDP

Parental  GGFGIAPHCLDEGTVRSMVTEEFNGSD-WEKAMKEHKTIKNMSKE
          ...G.APHCLDEGTVRS.V.EE..G.D..E.A..EHK.I...S..
Retrocopy RVYGVAPHCLDEGTVRSVVIEEVGGGDPGEEAAEEHKAIHKTSSQ

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
bodymap2_adipose	0.00 RPM	6.62 RPM
bodymap2_adrenal	0.00 RPM	10.97 RPM
bodymap2_brain	0.00 RPM	10.20 RPM
bodymap2_breast	0.00 RPM	5.82 RPM
bodymap2_colon	0.00 RPM	6.32 RPM
bodymap2_heart	0.00 RPM	2.97 RPM
bodymap2_kidney	0.00 RPM	7.36 RPM
bodymap2_liver	0.00 RPM	11.74 RPM
bodymap2_lung	0.00 RPM	6.00 RPM
bodymap2_lymph_node	0.00 RPM	3.58 RPM
bodymap2_ovary	0.00 RPM	17.12 RPM
bodymap2_prostate	0.00 RPM	8.90 RPM
bodymap2_skeletal_muscle	0.00 RPM	6.07 RPM
bodymap2_testis	0.00 RPM	19.95 RPM
bodymap2_thyroid	0.00 RPM	8.46 RPM
bodymap2_white_blood_cells	0.00 RPM	2.19 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4683 was not detected

EST

No EST(s) were mapped for retro_hsap_4683 retrocopy.

TSS

No TSS is located nearby retro_hsap_4683 retrocopy 5' end.

Lab

retro_hsap_4683 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4683 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004716	5 retrocopies	retro_amel_1859, retro_amel_1870, retro_amel_1909, retro_amel_1926, retro_amel_924,
Canis familiaris	ENSCAFG00000018019	2 retrocopies	retro_cfam_2153, retro_cfam_2155,
Homo sapiens	ENSG00000166582	3 retrocopies	retro_hsap_4683 , retro_hsap_4833, retro_hsap_4834,
Macropus eugenii	ENSMEUG00000002027	1 retrocopy	retro_meug_519,
Microcebus murinus	ENSMICG00000007166	1 retrocopy	retro_mmur_1491,
Mustela putorius furo	ENSMPUG00000010146	2 retrocopies	retro_mputfur_1195, retro_mputfur_39,
Nomascus leucogenys	ENSNLEG00000014726	1 retrocopy	retro_nleu_2709,
Otolemur garnettii	ENSOGAG00000029365	1 retrocopy	retro_ogar_99,
Pan troglodytes	ENSPTRG00000008810	1 retrocopy	retro_ptro_3216,
Ictidomys tridecemlineatus	ENSSTOG00000012221	2 retrocopies	retro_itri_110, retro_itri_1540,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

---

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).