RetrogeneDB ID: retro_hsap_152

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:52719292..52719748(+)
• Located in intron of: ENSG00000157077

Retrocopy information

• Ensembl ID: ENSG00000213735
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ANAPC10
• Ensembl ID: ENSG00000164162
• Aliases: None
• Description: anaphase promoting complex subunit 10 [Source:HGNC Symbol;Acc:24077]

Sequence

>retro_hsap_152
ATGACCACACCAAACAAGGCACCTCCTGGTACTGACCCTGAGCAGTTGGAAAAGACTGGAACAGTACGGGAAATTGGGTC
ACAAGCTGTTTGGTCACTCTCATCTTGCAAACCAGGATTTGGAGTGGATCAGTTACGAGATGACAATCTAGAAACTTATT
GGCAATCAGATGGCTCCCAGCCTCATTTAGTGAACATCCAATTCAGAAGAAAAACAACAGTTAAGACATTATATATTTAT
GCAGACTACAAATCTGATGAAAGCTATACTCCAAGCAAGATTTCAGCCAAAGTAGGAAATAATTTTCACAACCTTCAAGA
AATTCGGCAACTTGAATTGGTGGAACCAAGTGGCTGGATTCATATTCCCTTAACTGATAATCATAGGAAGCCAACTTGGA
CGTTAATGATACAGATTGCTGTTCTAGCCAGTCATCAAAATGGAAAAGACACCCAC

Alignment

ORF - retro_hsap_152 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.45 %
• Parental protein coverage: 96.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTPNKTPPGADPKQLERTGTVREIGSQAVWSLSSCKPGFGVDQLRDDNLETYWQSDGSQPHLVNIQFRR
          MTTPNK.PPG.DP.QLE.TGTVREIGSQAVWSLSSCKPGFGVDQLRDDNLETYWQSDGSQPHLVNIQFRR
Retrocopy MTTPNKAPPGTDPEQLEKTGTVREIGSQAVWSLSSCKPGFGVDQLRDDNLETYWQSDGSQPHLVNIQFRR

Parental  KTTVKTLCIYADYKSDESYTPSKISVRVGNNFHNLQEIRQLELVEPSGWIHVPLTDNHKKPTRTFMIQIA
          KTTVKTL.IYADYKSDESYTPSKIS..VGNNFHNLQEIRQLELVEPSGWIH.PLTDNH.KPT.T.MIQIA
Retrocopy KTTVKTLYIYADYKSDESYTPSKISAKVGNNFHNLQEIRQLELVEPSGWIHIPLTDNHRKPTWTLMIQIA

Parental  VLANHQNGRDTH
          VLA.HQNG.DTH
Retrocopy VLASHQNGKDTH

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	0.24 RPM	4.59 RPM
bodymap2_adrenal	0.04 RPM	8.09 RPM
bodymap2_brain	0.00 RPM	8.30 RPM
bodymap2_breast	0.10 RPM	8.29 RPM
bodymap2_colon	0.00 RPM	6.55 RPM
bodymap2_heart	0.00 RPM	5.19 RPM
bodymap2_kidney	0.00 RPM	11.85 RPM
bodymap2_liver	0.00 RPM	4.73 RPM
bodymap2_lung	0.00 RPM	6.91 RPM
bodymap2_lymph_node	0.00 RPM	7.71 RPM
bodymap2_ovary	0.04 RPM	8.64 RPM
bodymap2_prostate	0.00 RPM	11.48 RPM
bodymap2_skeletal_muscle	0.00 RPM	5.51 RPM
bodymap2_testis	0.06 RPM	18.80 RPM
bodymap2_thyroid	0.00 RPM	11.54 RPM
bodymap2_white_blood_cells	0.00 RPM	6.54 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_152 was not detected

EST

No EST(s) were mapped for retro_hsap_152 retrocopy.

TSS

No TSS is located nearby retro_hsap_152 retrocopy 5' end.

Lab

retro_hsap_152 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_152 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_149
Gorilla gorilla	retro_ggor_241
Pongo abelii	retro_pabe_468
Macaca mulatta	retro_mmul_374
Callithrix jacchus	retro_cjac_2999

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002663	2 retrocopies	retro_cjac_2683, retro_cjac_2999,
Dipodomys ordii	ENSDORG00000016690	1 retrocopy	retro_dord_202,
Homo sapiens	ENSG00000164162	1 retrocopy	retro_hsap_152 ,
Gorilla gorilla	ENSGGOG00000025091	1 retrocopy	retro_ggor_241,
Myotis lucifugus	ENSMLUG00000008607	1 retrocopy	retro_mluc_1679,
Macaca mulatta	ENSMMUG00000004432	1 retrocopy	retro_mmul_374,
Mus musculus	ENSMUSG00000036977	1 retrocopy	retro_mmus_1511,
Nomascus leucogenys	ENSNLEG00000005453	1 retrocopy	retro_nleu_1498,
Otolemur garnettii	ENSOGAG00000006902	2 retrocopies	retro_ogar_1649, retro_ogar_2510,
Pongo abelii	ENSPPYG00000015096	1 retrocopy	retro_pabe_468,
Pan troglodytes	ENSPTRG00000016480	1 retrocopy	retro_ptro_149,
Pteropus vampyrus	ENSPVAG00000013169	2 retrocopies	retro_pvam_1245, retro_pvam_1450,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.02 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	0.02 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.07 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 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	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.02 RPM

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Indel association:

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