RetrogeneDB ID: retro_hsap_4088

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:88588025..88588734(-)
• Located in intron of: ENSG00000176571

Retrocopy information

• Ensembl ID: ENSG00000253401
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VTA1
• Ensembl ID: ENSG00000009844
• Aliases: None
• Description: Vps20-associated 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20954]

Sequence

>retro_hsap_4088
ATGTTCATGATTGCTCTACTGTCCCCACTTCCTCCCCAGTTTAAGAGCATACAGCATCATATGAAAACAGCTCAGGAGCA
TGACAAGCCGGACCCCGCGGTGCTCTATTACTGTTGTTTCTATGCAATGCAAACCAGAATGAAGACTGATAGTAAAACTC
CTGAGAGTTGTACATTTTTATCAAAGCTAATGGATCAGTTAGAAATACTTATGAAACAGTTGGGTGATCATGAAGCTATT
AGGCAAGAAAATACTTAGTCCTGCCCATTTGGAGAACTATGCTTAGAAAATGTTTTTATACTCAGACAATGATCATGCTG
GGTGATTTCACAAGATGATCAAGCCCTTTTTATACTCCACAGTTTTAAATAGATGCCATAATAATATTAGGACAACTCAC
TGATGAAAATGTGAAACACAGAAAGTATGTAAGATGAAAAGCAAAATATATTCATATTTGTTTAAAGAATGGGGAGCTGC
CTCAACTAGTATCTGCTGGAATTGAAGAAGATAACAATATAACAATATTGCAGAAAATGAAAATGCTGAAGCAACCTATC
TGTCCACTGAGCCATGTCAGCCACCATCTTCAACTTATGACCCAAGCCACATGCCATAAAGGAGCTATAATAGAATACAG
ATTCCTCCCAGTGCACACACTCCAGCTAATACATCAGTAGAAGTGCATCACAATGCAGATGTAACAAAT

Alignment

ORF - retro_hsap_4088 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.49 %
• Parental protein coverage: 76.87 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAALAPLPPLPAQFKSIQHHLRTAQEHDKRDPVVAYYCRLYAMQTGMKIDSKTPECRKFLSKLMDQLEAL
          M...A.L.PLP.QFKSIQHH..TAQEHDK.DP.V.YYC..YAMQT.MK.DSKTPE...FLSKLMDQLE.L
Retrocopy MFMIALLSPLPPQFKSIQHHMKTAQEHDKPDPAVLYYCCFYAMQTRMKTDSKTPESCTFLSKLMDQLEIL

Parental  KKQLGDNEAITQE-IVGCAHLENYALKMFLYADNEDRAGRFHKNMIK-SFYTASLLIDVITVFGELTDEN
          .KQLGD.EAI.QE.I...AHLENYA.KMFLY.DN.D.AG.FHK.MIK..FYT....ID.I...G.LTDEN
Retrocopy MKQLGDHEAIRQE>ILSPAHLENYA*KMFLYSDN-DHAG*FHK-MIK>PFYTPQF*IDAIIILGQLTDEN

Parental  VKHRKYARWKATYIHNCLKNGETPQAGPVGIEEDNDIEENEDAGAASLPTQP-TQPSS--SSTYDPSNMP
          VKHRKY.R.KA.YIH.CLKNGE.PQ....GIEEDN.I...........P..P.T.P....SSTYDPS.MP
Retrocopy VKHRKYVR*KAKYIHICLKNGELPQLVSAGIEEDNNITILQKMKMLKQPICP<TEPCQPPSSTYDPSHMP

Parental  SGNYTGIQIPPGAHAPANTPAEVPHSTGVAS
          ...Y..IQIPP.AH.PANT..EV.H...V..
Retrocopy *RSYNRIQIPPSAHTPANTSVEVHHNADVTN

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	28.35 RPM
bodymap2_adrenal	0.00 RPM	32.91 RPM
bodymap2_brain	0.00 RPM	65.56 RPM
bodymap2_breast	0.00 RPM	38.76 RPM
bodymap2_colon	0.00 RPM	39.29 RPM
bodymap2_heart	0.00 RPM	32.82 RPM
bodymap2_kidney	0.00 RPM	51.89 RPM
bodymap2_liver	0.00 RPM	31.22 RPM
bodymap2_lung	0.00 RPM	25.83 RPM
bodymap2_lymph_node	0.00 RPM	37.24 RPM
bodymap2_ovary	0.00 RPM	40.69 RPM
bodymap2_prostate	0.00 RPM	50.21 RPM
bodymap2_skeletal_muscle	0.00 RPM	56.91 RPM
bodymap2_testis	0.00 RPM	41.31 RPM
bodymap2_thyroid	0.00 RPM	58.66 RPM
bodymap2_white_blood_cells	0.00 RPM	71.70 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4088 was not detected

EST

No EST(s) were mapped for retro_hsap_4088 retrocopy.

TSS

No TSS is located nearby retro_hsap_4088 retrocopy 5' end.

Lab

retro_hsap_4088 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4088 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2742

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000009844	1 retrocopy	retro_hsap_4088 ,
Gorilla gorilla	ENSGGOG00000015524	1 retrocopy	retro_ggor_2742,
Microcebus murinus	ENSMICG00000004420	2 retrocopies	retro_mmur_1290, retro_mmur_290,
Macaca mulatta	ENSMMUG00000023012	1 retrocopy	retro_mmul_751,
Nomascus leucogenys	ENSNLEG00000015053	1 retrocopy	retro_nleu_1911,
Oryctolagus cuniculus	ENSOCUG00000002554	10 retrocopies	retro_ocun_1543, retro_ocun_1689, retro_ocun_1790, retro_ocun_1810, retro_ocun_1821, retro_ocun_1832, retro_ocun_1848, retro_ocun_1853, retro_ocun_1864, retro_ocun_965,
Pan troglodytes	ENSPTRG00000018662	1 retrocopy	retro_ptro_2773,
Rattus norvegicus	ENSRNOG00000011540	1 retrocopy	retro_rnor_799,
Tursiops truncatus	ENSTTRG00000014998	1 retrocopy	retro_ttru_1825,

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).