RetrogeneDB ID: retro_hsap_594

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:75491654..75493157(+)
• Located in intron of: ENSG00000250959

Retrocopy information

• Ensembl ID: ENSG00000235316
• 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_594
GGGTGCCTGGTCATCTACAGCCGCTCCTTCCTGGAGTACAACAGCTGGCATGTGCTCAGCTCCGTCAACATCTGCTGCTC
CAAGCTGGTGAAGTGCCGGCTGCAGAAGGGCAAGGTGACCATTGCAGAGTTCATCTGGCTGGCCACACGCAGCCAAATGG
AGGCCACTGAGCCACAGGATATGGTGGTCTATGACCAGAGCACACGGGACGCCAGTGTGCTGGCCGCAGACCGCTTCCTC
TCCATCCTGCTGAGCAAGCTGGACAGCTGCTTCGACAGCGTGGCCATCCTCACGGGGGGCTTCGCCACCTTCTCCTCCTG
CTTCCCCAGCCTCTGCCAGGGCAAGCCTGCTGCCCTGCTACCCATGAGCCTCTCCCAGCCCTGCCTGCCCGTGCCTAGCG
TGAGCCTGACCCTCATCCTGCCTCACCTCTACCTGGGCTCGCAGAAAGACGTTCTGAACAAGGATCTGACGACACAGAAT
GGAATAAGCTACGTCCTCAATGCCAGCAACTCCTGCCCCAAGCCTGACTTCATCTGCGAGAGCCGCTTCATGCGGGTCCC
CATCAACGACAACTACTGTGAAAAGCTGCTGCCCTGGCTGGACAAGTCTATGGAGTTCATCTGTAAAGGCAAGCTGTCCA
GCTGCCAAGTCATCGTCCACTGTCTGGTCGGTATCTCCCACTCTGCCACCATCGCCATCGCCTACATCATGAAGACCATG
GGCATATCCTCCGACGACACCTACAGGTTCATGAAGGATAGGCGCCAGTCCATCTCGCCCAACTTCAACTTCCTGGGCCA
GCTGCTGGAGTAGGAGCGCAGCCTGAAGCTGCTGGCCACCGTGCAGGGGGATGCGGGCACCCCCTCAGGGACGCCGGAGC
CTCCGCCCAGCCCTGCGGCTGGGGCCCGGCTGCCATGGCTGCCACCACCTACCTCAGAAAGCGCTGCCACCGGGAGTGCA
GCTGCCAGGGAGGGCGGCCTGAGCGCGGGCGGGGAGCCCCCACTGCCCCCCACGCCCCCAGACACCTGCGCGCTGCAGCA
GGGCTGCGCGGCCTGTACTCTCCTCTGACCGCCTGCAGGACACCAACCGCCTCAAGCGCTCCTTCTCGCTGTACATCAAA
TCAGCGAACACCCCCGGCCGGCGGCCCAACGGCCCCGGGTCACCCGACCCCGGCGAGGTCCCAAAGCTCTGCAAGCTGCA
CGGCCCGTCGGAGCCACGCTGAGCCTACCTTCGCCCAGCCCCGACAGCCCGGATGCCGCGCGCCCACGGCCCTGCGGGCG
GCCCAGGCCCCCAGCCGGCTCCCCGCTCCCCCGCGCACAGCCTCGGCCTCTCGGCCCTGTCGGCGCCCAGGCTGCCCGGC
CCTGGCCAGCCGGCCCCGGAGTCTGGGCGCCACCGCTTGACTCCCCGGGCACGCCGTCGCCCGACGGGCCCTAGTGCTTC
AGCCCCGAGGGCGCGCAGGGGGCGGGCGGGGTGCTGTTCGCGCCCTTTGGCCAGGCGGGCGCC

Alignment

ORF - retro_hsap_594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 81.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GPLVIDSRSFVEYNSWHVLSSVNICCSKLVKRRLQQGKVTIAELIQPAARSQVEATEPQDVVVYDQSTRD
          G.LVI.SRSF.EYNSWHVLSSVNICCSKLVK.RLQ.GKVTIAE.I..A.RSQ.EATEPQD.VVYDQSTRD
Retrocopy GCLVIYSRSFLEYNSWHVLSSVNICCSKLVKCRLQKGKVTIAEFIWLATRSQMEATEPQDMVVYDQSTRD

Parental  ASVLAADSFLSILLSKLDGCFDSVAILTGGFATFSSCFPGLCEGKPAALLPMSLSQPCLPVPSVGLTRIL
          ASVLAAD.FLSILLSKLD.CFDSVAILTGGFATFSSCFP.LC.GKPAALLPMSLSQPCLPVPSV.LT.IL
Retrocopy ASVLAADRFLSILLSKLDSCFDSVAILTGGFATFSSCFPSLCQGKPAALLPMSLSQPCLPVPSVSLTLIL

Parental  PHLYLGSQKDVLNKDLMTQNGISYVLNASNSCPKPDFICESRFMRVPINDNYCEKLLPWLDKSIEFIDKA
          PHLYLGSQKDVLNKDL.TQNGISYVLNASNSCPKPDFICESRFMRVPINDNYCEKLLPWLDKS.EFI.K.
Retrocopy PHLYLGSQKDVLNKDLTTQNGISYVLNASNSCPKPDFICESRFMRVPINDNYCEKLLPWLDKSMEFICKG

Parental  KLSSCQVIVHCLAGISRSATIAIAYIMKTMGMSSDDAYRFVKDRRPSISPNFNFLGQLLEYERSLKLLAA
          KLSSCQVIVHCL.GIS.SATIAIAYIMKTMG.SSDD.YRF.KDRR.SISPNFNFLGQLLE.ERSLKLLA.
Retrocopy KLSSCQVIVHCLVGISHSATIAIAYIMKTMGISSDDTYRFMKDRRQSISPNFNFLGQLLE*ERSLKLLAT

Parental  LQGDPGTPSGTPEPPPSPAAGAPLPRLPPPTSESAATGNAAAREGGLSAGGEPPAPPTPPATSALQQ-GL
          .QGD.GTPSGTPEPPPSPAAGA.LP.LPPPTSESAATG.AAAREGGLSAGG..........T.ALQQ.GL
Retrocopy VQGDAGTPSGTPEPPPSPAAGARLPWLPPPTSESAATGSAAAREGGLSAGGXXXXXXXXXDTCALQQ<GL

Parental  RGLH-LSSDRLQDTNRLKRSFSLDIKSAYAPSRRPDGPGPPDPGEAPKLCKLDSPS-GAALGLSSPSPDS
          RGL..LSSDRLQDTNRLKRSFSL.IKSA..P.RRP.GPG.PDPGE.PKLCKL..PS.GA.L.L.SPSPDS
Retrocopy RGLY<LSSDRLQDTNRLKRSFSLYIKSANTPGRRPNGPGSPDPGEVPKLCKLHGPS<GATLSLPSPSPDS

Parental  PDAAPEARPRPRRRPRPPAGSP-ARSPAHSLGLNFGDAARQTPRHGLSALSAPGLPGPGQPAGPGAWAPP
          PDAA...RPRP..RPRPPAGSP..R.....LG.....AAR..P..G......P.L..PG.P...G...P.
Retrocopy PDAA---RPRPCGRPRPPAGSPLPRAQPRPLGPVGAQAARPWPA-GPGVWAPP-LDSPGTPSPDG---P*

Parental  LDSPGTPSPDGPWCFSPEGAQGA
          ..SP......G...F.P.G..GA
Retrocopy CFSPEGAQGAGGVLFAPFGQAGA

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	0.50 RPM	7.28 RPM
bodymap2_adrenal	2.17 RPM	2.27 RPM
bodymap2_brain	0.70 RPM	32.44 RPM
bodymap2_breast	0.41 RPM	6.71 RPM
bodymap2_colon	0.14 RPM	4.76 RPM
bodymap2_heart	0.33 RPM	12.24 RPM
bodymap2_kidney	0.45 RPM	3.93 RPM
bodymap2_liver	0.15 RPM	0.04 RPM
bodymap2_lung	0.46 RPM	19.83 RPM
bodymap2_lymph_node	0.51 RPM	3.82 RPM
bodymap2_ovary	0.44 RPM	4.99 RPM
bodymap2_prostate	0.78 RPM	20.35 RPM
bodymap2_skeletal_muscle	0.62 RPM	16.02 RPM
bodymap2_testis	0.38 RPM	7.32 RPM
bodymap2_thyroid	1.19 RPM	4.05 RPM
bodymap2_white_blood_cells	0.20 RPM	1.85 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_594 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CHO	POLR2A	10:75489861..75490688
ENCFF002CMI	POLR2A	10:75489858..75490672

EST

9 EST(s) were mapped to retro_hsap_594 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CA394418	75491613	75492280	100	667	0	667
CD357049	75492134	75492271	97.9	134	3	131
CN418889	75491636	75492136	100	499	0	498
CN418890	75491741	75491954	100	213	0	213
CN418891	75491745	75492445	99.9	699	1	698
HY011002	75492191	75492680	98.8	481	5	473
HY187789	75492281	75492619	99.8	335	1	334
HY262530	75491711	75492198	99.6	485	2	483
HY297734	75491749	75492198	99.8	448	1	447

TSS

No TSS is located nearby retro_hsap_594 retrocopy 5' end.

Lab

retro_hsap_594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_594 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	1.01 RPM
CEU_NA11843	0.71 RPM
CEU_NA11930	1.60 RPM
CEU_NA12004	0.49 RPM
CEU_NA12400	0.53 RPM
CEU_NA12751	1.72 RPM
CEU_NA12760	1.66 RPM
CEU_NA12827	1.51 RPM
CEU_NA12872	0.90 RPM
CEU_NA12873	1.02 RPM
FIN_HG00183	1.65 RPM
FIN_HG00277	1.59 RPM
FIN_HG00315	0.88 RPM
FIN_HG00321	1.36 RPM
FIN_HG00328	0.62 RPM
FIN_HG00338	0.51 RPM
FIN_HG00349	0.37 RPM
FIN_HG00375	1.39 RPM
FIN_HG00377	0.53 RPM
FIN_HG00378	0.81 RPM
GBR_HG00099	0.64 RPM
GBR_HG00111	0.71 RPM
GBR_HG00114	1.34 RPM
GBR_HG00119	1.39 RPM
GBR_HG00131	1.67 RPM
GBR_HG00133	1.01 RPM
GBR_HG00134	2.03 RPM
GBR_HG00137	1.48 RPM
GBR_HG00142	1.25 RPM
GBR_HG00143	0.80 RPM
TSI_NA20512	0.54 RPM
TSI_NA20513	0.89 RPM
TSI_NA20518	1.05 RPM
TSI_NA20532	1.80 RPM
TSI_NA20538	1.38 RPM
TSI_NA20756	0.29 RPM
TSI_NA20765	1.39 RPM
TSI_NA20771	1.16 RPM
TSI_NA20786	0.42 RPM
TSI_NA20798	1.53 RPM
YRI_NA18870	1.39 RPM
YRI_NA18907	1.46 RPM
YRI_NA18916	0.95 RPM
YRI_NA19093	0.94 RPM
YRI_NA19099	0.40 RPM
YRI_NA19114	0.42 RPM
YRI_NA19118	0.97 RPM
YRI_NA19213	0.67 RPM
YRI_NA19214	0.91 RPM
YRI_NA19223	1.63 RPM

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Indel association:

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