RetrogeneDB ID: retro_hsap_3455

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:34991296..34991601(+)
• Located in intron of: ENSG00000064999

Retrocopy information

• Ensembl ID: ENSG00000187762
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HSPE1
• Ensembl ID: ENSG00000115541
• Aliases: HSPE1, CPN10, EPF, GROES, HSP10
• Description: heat shock 10kDa protein 1 (chaperonin 10) [Source:HGNC Symbol;Acc:5269]

Sequence

>retro_hsap_3455
ATGGCGGGACCAGCATTTAGAAAGTTTCTTTCACTCTTTGACTGAATATTGGTTGAAAGGAGTGCAGCTGAAACTGTAAC
CAAAGGAGGCATTATGCCTCCAGGAAAATCTCAGGGAGAAGTATCACAAGCAGCAGTGGTAGCTGTTGGATCAGGCTCTA
AAGGAAAGGGTAGAGAGATTCGACCAATTAGCGTGGAAGTTGGAGACAAATTTCTTCTCCCAGAATATAGAGGCACCAAA
GTAGTTCTAGGTGACAGGATTATTTCTTATTTAGAGATGGTGACATTCTTGGAAAGAATGCAGAC

Alignment

ORF - retro_hsap_3455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.58 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGQAFRKFLPLFDRVLVERSAAETVTKGGIMLPEKSQGKVLQATVVAVGSGSKGKGGEIQPVSVKVGDK
          MAG.AFRKFL.LFD..LVERSAAETVTKGGIM.P.KSQG.V.QA.VVAVGSGSKGKG.EI.P.SV.VGDK
Retrocopy MAGPAFRKFLSLFD*ILVERSAAETVTKGGIMPPGKSQGEVSQAAVVAVGSGSKGKGREIRPISVEVGDK

Parental  VLLPEYGGTKVVLDDK-DYFLFRDGDILGKYVD
          .LLPEY.GTKVVL.D..DYFLFRDGDILGK..D
Retrocopy FLLPEYRGTKVVLGDR<DYFLFRDGDILGKNAD

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	0.30 RPM	21.55 RPM
bodymap2_adrenal	0.10 RPM	44.48 RPM
bodymap2_brain	0.07 RPM	61.79 RPM
bodymap2_breast	0.06 RPM	45.72 RPM
bodymap2_colon	0.00 RPM	87.78 RPM
bodymap2_heart	0.11 RPM	19.22 RPM
bodymap2_kidney	0.00 RPM	94.55 RPM
bodymap2_liver	0.04 RPM	89.42 RPM
bodymap2_lung	0.07 RPM	41.81 RPM
bodymap2_lymph_node	0.26 RPM	56.39 RPM
bodymap2_ovary	0.06 RPM	72.73 RPM
bodymap2_prostate	0.00 RPM	32.84 RPM
bodymap2_skeletal_muscle	0.00 RPM	12.90 RPM
bodymap2_testis	0.15 RPM	56.35 RPM
bodymap2_thyroid	0.06 RPM	105.98 RPM
bodymap2_white_blood_cells	0.00 RPM	13.53 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3455 was not detected

EST

No EST(s) were mapped for retro_hsap_3455 retrocopy.

TSS

No TSS is located nearby retro_hsap_3455 retrocopy 5' end.

Lab

retro_hsap_3455 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3455 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2343
Gorilla gorilla	retro_ggor_2331

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004008	1 retrocopy	retro_cjac_254,
Dasypus novemcinctus	ENSDNOG00000013246	27 retrocopies	retro_dnov_1088, retro_dnov_1117, retro_dnov_1214, retro_dnov_1375, retro_dnov_1391, retro_dnov_1405, retro_dnov_1412, retro_dnov_1428, retro_dnov_1445, retro_dnov_1546, retro_dnov_1647, retro_dnov_1652, retro_dnov_1686, retro_dnov_1821, retro_dnov_2176, retro_dnov_2291, retro_dnov_2413, retro_dnov_2569, retro_dnov_2625, retro_dnov_2652, retro_dnov_418, retro_dnov_481, retro_dnov_483, retro_dnov_490, retro_dnov_524, retro_dnov_554, retro_dnov_966,
Homo sapiens	ENSG00000115541	18 retrocopies	retro_hsap_1066, retro_hsap_1152, retro_hsap_1351, retro_hsap_1524, retro_hsap_1646, retro_hsap_1703, retro_hsap_2248, retro_hsap_2402, retro_hsap_2480, retro_hsap_2812, retro_hsap_2813, retro_hsap_3455 , retro_hsap_3540, retro_hsap_366, retro_hsap_3664, retro_hsap_4194, retro_hsap_495, retro_hsap_963,
Procavia capensis	ENSPCAG00000009541	1 retrocopy	retro_pcap_330,
Sus scrofa	ENSSSCG00000016078	7 retrocopies	retro_sscr_103, retro_sscr_1059, retro_sscr_106, retro_sscr_1088, retro_sscr_294, retro_sscr_298, retro_sscr_401,

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	0.00 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.11 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.10 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.06 RPM

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Indel association:

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