RetrogeneDB ID: retro_hsap_1900

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 18:1362541..1363318(-)
• Located in intron of: ENSG00000132204

Retrocopy information

• Ensembl ID: ENSG00000265417
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATAD1
• Ensembl ID: ENSG00000138138
• Aliases: ATAD1, AFDC1, THORASE
• Description: ATPase family, AAA domain containing 1 [Source:HGNC Symbol;Acc:25903]

Sequence

>retro_hsap_1900
GTAGACCCTCTTAATATGCATGTTACTTGGAAGTGATATAGCAGGTTTAGATGAGGTCATTACGGATCTGAAAGACAGTC
ATCTTACCTATCAAAAAGAAACATTTGTTTGAGAATTCCAGGCTTCTGCAGCCTCCAAAAGGTGTTCTTCTCTATGAGCC
TCCCCAGGCTGTGGTAAAACGTTGATTGCCAAGGCCACAGCCAAAGAAGCAGGCTGTCGATTTATTAACCTTGAGCCTTC
GACACTGACCAATAAGTGGTATGGAGAATCTCAAACACTGGCTGCTGCTGTCTTCTCCCTTGCCATAAAGCTACAACTGT
CCATCATCATTATAGACGAAATAGACTCCTTTGTACGAAACCGTTCAGAGTTCTGACCATGAAGCTACAGCCATAATGAA
AGCTCAGTTTATGAGTCTCTGGGATGGACTGGACACTGATCACCGCTGCCAGGTCATAGTAATGGGAGCTACCATTCATC
CTCAGGACATTGACACGGCTATAACGAGAAGAATTCCTACAAGATTTCACATCAACCAGCCTGCTTTAAAACAGAAAGAA
GCAATCCTGAAACTCATCTTGAAAAATGAAAATGTGGATAGGCATGTAGACCTGCTAGAAGTTGCCCAGGAAACTGATGC
GTTTTCAGGAAGGGACCTAAATGCGATGTGTTGAGATGCTGCCCTCCTCTGTGTTAGAGAATGTTAATTCTACATCAGAA
GAAAGCCATGATGAAGATGAAATTCGGCCTGTTCAACAGCAGGACCTGCATCGGGCA

Alignment

ORF - retro_hsap_1900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.95 %
• Parental protein coverage: 71.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VDPLNMHVTW-SDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGVLLYGPPGCGKTLIAKATAKE
          VDPLNMHVTW.SDIAGLD.VITDLKD......K.....E............L...PGCGKTLIAKATAKE
Retrocopy VDPLNMHVTW>SDIAGLDEVITDLKDSHLTYQKETFV*EFQASAASKRCSSL*ASPGCGKTLIAKATAKE

Parental  AGCRFINLQPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLRNRS-SSDHEATAMMKAQFMS
          AGCRFINL.PSTLT.KWYGESQ.LAAAVFSLAIKLQ.SII.IDEIDSF.RNRS.SSDHEATA.MKAQFMS
Retrocopy AGCRFINLEPSTLTNKWYGESQTLAAAVFSLAIKLQLSIIIIDEIDSFVRNRS>SSDHEATAIMKAQFMS

Parental  LWDGLDTDHSCQVIVMGATNRPQDLDSAIMRRMPTRFHINQPALKQREAILKLILKNENVDRHVDLLEVA
          LWDGLDTDH.CQVIVMGAT..PQD.D.AI.RR.PTRFHINQPALKQ.EAILKLILKNENVDRHVDLLEVA
Retrocopy LWDGLDTDHRCQVIVMGATIHPQDIDTAITRRIPTRFHINQPALKQKEAILKLILKNENVDRHVDLLEVA

Parental  QETDGFSGSDLKEMCRDAALLCVRE-YVNSTSEESHDEDEIRPVQQQDLHRA
          QETD.FSG.DL..MC.DAALLCVRE.......E.......IRPVQQQDLHRA
Retrocopy QETDAFSGRDLNAMC*DAALLCVRE>VNSTSEESHDEDE-IRPVQQQDLHRA

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	50.33 RPM
bodymap2_adrenal	0.00 RPM	44.19 RPM
bodymap2_brain	0.00 RPM	97.79 RPM
bodymap2_breast	0.00 RPM	78.23 RPM
bodymap2_colon	0.00 RPM	82.25 RPM
bodymap2_heart	0.02 RPM	112.48 RPM
bodymap2_kidney	0.15 RPM	84.58 RPM
bodymap2_liver	0.00 RPM	29.57 RPM
bodymap2_lung	0.00 RPM	71.13 RPM
bodymap2_lymph_node	0.00 RPM	52.83 RPM
bodymap2_ovary	0.00 RPM	72.08 RPM
bodymap2_prostate	0.00 RPM	82.32 RPM
bodymap2_skeletal_muscle	0.02 RPM	69.93 RPM
bodymap2_testis	0.15 RPM	121.58 RPM
bodymap2_thyroid	0.00 RPM	68.73 RPM
bodymap2_white_blood_cells	0.00 RPM	59.34 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1900 was not detected

EST

No EST(s) were mapped for retro_hsap_1900 retrocopy.

TSS

No TSS is located nearby retro_hsap_1900 retrocopy 5' end.

Lab

retro_hsap_1900 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1900 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1255
Gorilla gorilla	retro_ggor_1393
Callithrix jacchus	retro_cjac_1101

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005296	1 retrocopy	retro_cjac_1101,
Homo sapiens	ENSG00000138138	1 retrocopy	retro_hsap_1900 ,
Gorilla gorilla	ENSGGOG00000026651	1 retrocopy	retro_ggor_1393,
Macaca mulatta	ENSMMUG00000006414	1 retrocopy	retro_mmul_608,
Nomascus leucogenys	ENSNLEG00000012135	1 retrocopy	retro_nleu_1231,
Oryctolagus cuniculus	ENSOCUG00000012082	1 retrocopy	retro_ocun_1634,
Pan troglodytes	ENSPTRG00000002717	1 retrocopy	retro_ptro_1255,
Pteropus vampyrus	ENSPVAG00000014020	1 retrocopy	retro_pvam_1080,
Rattus norvegicus	ENSRNOG00000010861	1 retrocopy	retro_rnor_2752,
Ictidomys tridecemlineatus	ENSSTOG00000006563	1 retrocopy	retro_itri_309,

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	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.02 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	0.00 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.02 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	0.03 RPM
TSI_NA20798	0.12 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.06 RPM
YRI_NA19213	0.36 RPM
YRI_NA19214	0.02 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).