RetrogeneDB ID: retro_hsap_1165

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:132611006..132611329(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000256804
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PLAC8
• Ensembl ID: ENSG00000145287
• Aliases: PLAC8, C15, onzin
• Description: placenta-specific 8 [Source:HGNC Symbol;Acc:19254]

Sequence

>retro_hsap_1165
GAGGCGCCGATGGTCGTTGTGGGAGTCGGTCTCGGTCCGGCACCCCAGAACTCCAACTGGCAGACAGGCATGTGTGACTG
CTTCAGCGACTGTGGAGTCTGCCTCTGTGGCACGTTTTGTTTCCCGTGCCTTGGGTGTCAAGTTGCAGCTGATATGAATG
AATGCTGTGTGGAGCAAGCGTCGCAATGAGGACTCTCTACAGGACGTGATATGGCATCCCTGGATCTATTTGTGATGATT
ATATGGCAACCCTTTGCGGTCCTCCTTGTACTCTTTGCCAAATCAAGAGAGATATCAACAGAAGGAGAGTCATGCGTACT
TTC

Alignment

ORF - retro_hsap_1165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.5 %
• Parental protein coverage: 97.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QAPVVVVTQPGVGPGPAPQNSNWQTGMCDCFSDCGVCLCGTFCFPCLGCQVAADMNECC-LCGTSVAMRT
          .AP.VVV...GVG.GPAPQNSNWQTGMCDCFSDCGVCLCGTFCFPCLGCQVAADMNE.C.LCG.SVAMRT
Retrocopy EAPMVVV---GVGLGPAPQNSNWQTGMCDCFSDCGVCLCGTFCFPCLGCQVAADMNE-C<LCGASVAMRT

Parental  LYRTRYGIPGSICDDYMATLCCPHCTLCQIKRDINRRRAMRTF
          LYRT.YGIPGSICDDYMATLC.P.CTLCQIKRDINRRR.MRTF
Retrocopy LYRT*YGIPGSICDDYMATLCGPPCTLCQIKRDINRRRVMRTF

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	0.20 RPM	3.52 RPM
bodymap2_adrenal	0.41 RPM	25.48 RPM
bodymap2_brain	0.42 RPM	0.75 RPM
bodymap2_breast	0.14 RPM	0.95 RPM
bodymap2_colon	0.33 RPM	5.55 RPM
bodymap2_heart	0.18 RPM	0.30 RPM
bodymap2_kidney	0.17 RPM	0.43 RPM
bodymap2_liver	0.28 RPM	4.88 RPM
bodymap2_lung	0.21 RPM	31.40 RPM
bodymap2_lymph_node	0.44 RPM	31.76 RPM
bodymap2_ovary	0.52 RPM	2.37 RPM
bodymap2_prostate	0.40 RPM	1.16 RPM
bodymap2_skeletal_muscle	0.18 RPM	0.24 RPM
bodymap2_testis	0.53 RPM	0.66 RPM
bodymap2_thyroid	0.21 RPM	0.75 RPM
bodymap2_white_blood_cells	0.06 RPM	142.19 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1165 was not detected

EST

No EST(s) were mapped for retro_hsap_1165 retrocopy.

TSS

No TSS is located nearby retro_hsap_1165 retrocopy 5' end.

Lab

retro_hsap_1165 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1165 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_800

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000145287	1 retrocopy	retro_hsap_1165 ,
Gorilla gorilla	ENSGGOG00000007464	1 retrocopy	retro_ggor_910,
Monodelphis domestica	ENSMODG00000019309	1 retrocopy	retro_mdom_950,
Mus musculus	ENSMUSG00000029322	1 retrocopy	retro_mmus_1051,
Otolemur garnettii	ENSOGAG00000017232	1 retrocopy	retro_ogar_714,
Pan troglodytes	ENSPTRG00000016226	1 retrocopy	retro_ptro_800,
Rattus norvegicus	ENSRNOG00000002217	2 retrocopies	retro_rnor_1489, retro_rnor_1878,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.30 RPM
CEU_NA11843	0.43 RPM
CEU_NA11930	0.88 RPM
CEU_NA12004	0.19 RPM
CEU_NA12400	0.39 RPM
CEU_NA12751	0.83 RPM
CEU_NA12760	0.63 RPM
CEU_NA12827	0.80 RPM
CEU_NA12872	0.65 RPM
CEU_NA12873	0.70 RPM
FIN_HG00183	0.71 RPM
FIN_HG00277	0.85 RPM
FIN_HG00315	0.66 RPM
FIN_HG00321	0.63 RPM
FIN_HG00328	0.21 RPM
FIN_HG00338	0.45 RPM
FIN_HG00349	0.51 RPM
FIN_HG00375	0.71 RPM
FIN_HG00377	0.55 RPM
FIN_HG00378	0.57 RPM
GBR_HG00099	0.46 RPM
GBR_HG00111	0.26 RPM
GBR_HG00114	0.55 RPM
GBR_HG00119	0.53 RPM
GBR_HG00131	0.63 RPM
GBR_HG00133	0.51 RPM
GBR_HG00134	0.81 RPM
GBR_HG00137	0.55 RPM
GBR_HG00142	0.61 RPM
GBR_HG00143	0.57 RPM
TSI_NA20512	0.28 RPM
TSI_NA20513	1.11 RPM
TSI_NA20518	0.50 RPM
TSI_NA20532	1.16 RPM
TSI_NA20538	0.41 RPM
TSI_NA20756	0.26 RPM
TSI_NA20765	1.12 RPM
TSI_NA20771	0.51 RPM
TSI_NA20786	0.50 RPM
TSI_NA20798	0.87 RPM
YRI_NA18870	0.34 RPM
YRI_NA18907	0.49 RPM
YRI_NA18916	0.59 RPM
YRI_NA19093	0.16 RPM
YRI_NA19099	0.56 RPM
YRI_NA19114	0.13 RPM
YRI_NA19118	0.29 RPM
YRI_NA19213	0.53 RPM
YRI_NA19214	0.52 RPM
YRI_NA19223	0.86 RPM

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Indel association:

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