RetrogeneDB ID: retro_hsap_669

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:48173744..48174742(-)
• Located in intron of: ENSG00000231209

Retrocopy information

• Ensembl ID: ENSG00000215024
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DUSP8
• Ensembl ID: ENSG00000184545
• Aliases: DUSP8, C11orf81, HB5, HVH-5, HVH8
• Description: dual specificity phosphatase 8 [Source:HGNC Symbol;Acc:3074]

Sequence

>retro_hsap_669
ATCATCACGGGGGGCTTCGCCACCTTCTCCTCCTGCTTCCCCGACCTCTGCAAGGGTGAGCCTGCTGCCCTGCTACCCAT
GAGCCTCTCCCAGTCCTGCCTGCTCGTGCCCAGCGTGGGCCTGACCCTCATCCTGCCTCACCTCTACCTGGGCTCGCAGG
AAGACGTCCTGAACAAGGATCTGATGACGCAGAATGGAATAAGCTACGTCCTCTATGCCAGCAACTCCTGCCCCAAGCCT
GACTTCATCTACCAGAGCCACTTCTTGCGGGTCCCCATCAACGACAACTACTGTGAAAAGCTGCTGCCCTGGCTGGACAA
GTCCATCGAGTTCGTCGATAAAGCCAAGCTGTCCAGCTGCCAAGTCATCGTCCACCGTCTGGCCGGCATCTCCTGCTGTG
CCACTATCGCCATCGCCTACATCATGAAGACCATGGGCATGTCCTCCGAAGACGCCTACAGGTTTGTGAAGGACCAGCGC
CCGTCCATCTCGCCCAACTTCAACTTCCTGGGCCAGCTGCTGGAGGACCAGAGCAGCCCGAAGCTGCTGGCCGCCGTGCA
GGGCGACGCGGGCACCCCCTCAGGAATGCAGGAGCCTCCCCCCAGCCCTGCGGCCGGGGCCCCACTGCCATGGCTGCCAC
CACCTACCTCAGAGACCGCTGCCACCAGGAGTGCAGCTGCCAGGGAGGGCGGCCCGAGCGCGGGCAGGAAGCCCCCGGCG
CCCCCCACGGCCACCAGCACGCTGCAGCAGGGCCTGCGCAGCCTGCGCCTCTCCTCGGACCACCTGCAGGACACCAGCCG
CCTCAAGCCCTCCTTCTCTCTGGACATCAAGTCGGCCTACGCCCCCAGCAGGCGGCCCGGCGGCCCGGGCCCAGCGACCC
CGGCGAGGCCCCGAAGCTCTCTGAAAGCTGGACAGCCAGTCGGGGCCATGCTGGGCCTGCCCTCGCCCTGCCCGGACGCC
GCGCCCAGGCACGCCCACGGCCCGGCGCGCTACCCCGC

Alignment

ORF - retro_hsap_669 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 54.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ILTGGFATFSSCFPGLCEGKPAALLPMSLSQPCLPVPSVGLTRILPHLYLGSQKDVLNKDLMTQNGISYV
          I.TGGFATFSSCFP.LC.G.PAALLPMSLSQ.CL.VPSVGLT.ILPHLYLGSQ.DVLNKDLMTQNGISYV
Retrocopy IITGGFATFSSCFPDLCKGEPAALLPMSLSQSCLLVPSVGLTLILPHLYLGSQEDVLNKDLMTQNGISYV

Parental  LNASNSCPKPDFICESRFMRVPINDNYCEKLLPWLDKSIEFIDKAKLSSCQVIVHCLAGISRSATIAIAY
          L.ASNSCPKPDFI..S.F.RVPINDNYCEKLLPWLDKSIEF.DKAKLSSCQVIVH.LAGIS..ATIAIAY
Retrocopy LYASNSCPKPDFIYQSHFLRVPINDNYCEKLLPWLDKSIEFVDKAKLSSCQVIVHRLAGISCCATIAIAY

Parental  IMKTMGMSSDDAYRFVKDRRPSISPNFNFLGQLLEYERSLKLLAALQGDPGTPSGTPEPPPSPAAGAPLP
          IMKTMGMSS.DAYRFVKD.RPSISPNFNFLGQLLE...S.KLLAA.QGD.GTPSG..EPPPSPAAGAPLP
Retrocopy IMKTMGMSSEDAYRFVKDQRPSISPNFNFLGQLLEDQSSPKLLAAVQGDAGTPSGMQEPPPSPAAGAPLP

Parental  RLPPPTSESAATGNAAAREGGLSAGGEPPAPPTPPATSALQQGLRGLHLSSDRLQDTNRLKRSFSLDIKS
          .LPPPTSE.AAT..AAAREGG.SAG..PPAPPT..ATS.LQQGLR.L.LSSD.LQDT.RLK.SFSLDIKS
Retrocopy WLPPPTSETAATRSAAAREGGPSAGRKPPAPPT--ATSTLQQGLRSLRLSSDHLQDTSRLKPSFSLDIKS

Parental  AYAPSRRPDG-PGPPDPGEAPKL-CKLDSPSGAALGLSSPSPDSPDAAP-EARPRPRRRPR
          AYAPSRRP.G.PGP.DPGEAPKL..K...P.GA.LGL.SP.PD...AAP..ARPRP...PR
Retrocopy AYAPSRRPGG<PGPSDPGEAPKL>LKAGQPVGAMLGLPSPCPD---AAP<QARPRPGALPR

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	7.28 RPM
bodymap2_adrenal	0.00 RPM	2.27 RPM
bodymap2_brain	0.00 RPM	32.44 RPM
bodymap2_breast	0.00 RPM	6.71 RPM
bodymap2_colon	0.00 RPM	4.76 RPM
bodymap2_heart	0.00 RPM	12.24 RPM
bodymap2_kidney	0.00 RPM	3.93 RPM
bodymap2_liver	0.00 RPM	0.04 RPM
bodymap2_lung	0.00 RPM	19.83 RPM
bodymap2_lymph_node	0.00 RPM	3.82 RPM
bodymap2_ovary	0.00 RPM	4.99 RPM
bodymap2_prostate	0.00 RPM	20.35 RPM
bodymap2_skeletal_muscle	0.00 RPM	16.02 RPM
bodymap2_testis	0.00 RPM	7.32 RPM
bodymap2_thyroid	0.00 RPM	4.05 RPM
bodymap2_white_blood_cells	0.00 RPM	1.85 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_669 was not detected

EST

No EST(s) were mapped for retro_hsap_669 retrocopy.

TSS

No TSS is located nearby retro_hsap_669 retrocopy 5' end.

Lab

retro_hsap_669 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_669 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000184545	5 retrocopies	retro_hsap_567, retro_hsap_569, retro_hsap_572, retro_hsap_594, retro_hsap_669 ,
Pongo abelii	ENSPPYG00000002903	2 retrocopies	retro_pabe_3541, retro_pabe_650,

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

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Indel association:

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