RetrogeneDB ID: retro_hsap_165

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:65407663..65407998(+)
• Located in intron of: ENSG00000162434

Retrocopy information

• Ensembl ID: ENSG00000233877
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ADI1
• Ensembl ID: ENSG00000182551
• Aliases: ADI1, APL1, ARD, Fe-ARD, MTCBP1, Ni-ARD, SIPL, mtnD
• Description: acireductone dioxygenase 1 [Source:HGNC Symbol;Acc:30576]

Sequence

>retro_hsap_165
GACAAATACAAGAACGATCCAGAATTATATAAAAATCCAAAGAGAGAGAAACTACTCCTGGATGAACATAATAACAATAT
GCAAAGATAAATTACCAAATTAGAGGAAAAGATGATGTCTTATGAGAAACATTTACATTTGAATGATGAAATTCGATATA
TCTTGGATGGAAGTAGGTATTTTGACATAAAAGATATAGAGGACACATGGATCTGAATTGCCAGGGAGAAAAAGATATAC
ATATACTTCGTGTGGGAATTTATCATCATTTCACTCTGGATGAAAAGTACTATGCAGAGACAATCTGGCCCTTTGCTAGA
TAACCGGTATGAACC

Alignment

ORF - retro_hsap_165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.52 %
• Parental protein coverage: 65.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DKYENDPELEK-IRRERNYSWMDIITICKDKLPN-YEEKIKMFYEEHLHLDDEIRYILDGSGYFDVRDKE
          DKY.NDPEL.K.I.RERNYSWM.IITICKDKLPN..EEK..M.YE.HLHL.DEIRYILDGS.YFD..D.E
Retrocopy DKYKNDPELYK>IQRERNYSWMNIITICKDKLPN<LEEKM-MSYEKHLHLNDEIRYILDGSRYFDIKDIE

Parental  DQWIRIFMEK-GDMVTLPAGIYHRFTVDEKNYTKAMRLFVGEPVWT
          D.WI.I..EK..D...L..GIYH.FT.DEK.Y......F...PV.T
Retrocopy DTWI*IAREK<KDIHILRVGIYHHFTLDEKYYAETIWPFAR*PV*T

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	45.10 RPM
bodymap2_adrenal	0.10 RPM	66.22 RPM
bodymap2_brain	0.00 RPM	44.68 RPM
bodymap2_breast	0.04 RPM	96.81 RPM
bodymap2_colon	0.00 RPM	69.51 RPM
bodymap2_heart	0.02 RPM	113.37 RPM
bodymap2_kidney	0.00 RPM	160.01 RPM
bodymap2_liver	0.00 RPM	299.89 RPM
bodymap2_lung	0.00 RPM	49.86 RPM
bodymap2_lymph_node	0.00 RPM	68.75 RPM
bodymap2_ovary	0.06 RPM	53.09 RPM
bodymap2_prostate	0.00 RPM	111.52 RPM
bodymap2_skeletal_muscle	0.00 RPM	48.36 RPM
bodymap2_testis	0.00 RPM	68.38 RPM
bodymap2_thyroid	0.24 RPM	66.08 RPM
bodymap2_white_blood_cells	0.00 RPM	66.07 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_165 was not detected

EST

No EST(s) were mapped for retro_hsap_165 retrocopy.

TSS

No TSS is located nearby retro_hsap_165 retrocopy 5' end.

Lab

retro_hsap_165 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_165 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_157
Gorilla gorilla	retro_ggor_250
Pongo abelii	retro_pabe_463

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018432	2 retrocopies	retro_amel_1306, retro_amel_1350,
Canis familiaris	ENSCAFG00000003257	3 retrocopies	retro_cfam_1764, retro_cfam_554, retro_cfam_603,
Choloepus hoffmanni	ENSCHOG00000010496	8 retrocopies	retro_chof_1146, retro_chof_1212, retro_chof_1800, retro_chof_2067, retro_chof_2163, retro_chof_401, retro_chof_742, retro_chof_748,
Dasypus novemcinctus	ENSDNOG00000007523	3 retrocopies	retro_dnov_181, retro_dnov_1891, retro_dnov_2106,
Equus caballus	ENSECAG00000005765	1 retrocopy	retro_ecab_870,
Echinops telfairi	ENSETEG00000015860	1 retrocopy	retro_etel_1732,
Felis catus	ENSFCAG00000025763	2 retrocopies	retro_fcat_1465, retro_fcat_882,
Homo sapiens	ENSG00000182551	2 retrocopies	retro_hsap_165 , retro_hsap_2427,
Gorilla gorilla	ENSGGOG00000034855	2 retrocopies	retro_ggor_1510, retro_ggor_250,
Loxodonta africana	ENSLAFG00000004902	1 retrocopy	retro_lafr_173,
Macaca mulatta	ENSMMUG00000019471	1 retrocopy	retro_mmul_622,
Monodelphis domestica	ENSMODG00000014484	2 retrocopies	retro_mdom_1128, retro_mdom_723,
Nomascus leucogenys	ENSNLEG00000007518	2 retrocopies	retro_nleu_1559, retro_nleu_237,
Oryctolagus cuniculus	ENSOCUG00000000530	1 retrocopy	retro_ocun_1236,
Otolemur garnettii	ENSOGAG00000007668	2 retrocopies	retro_ogar_2871, retro_ogar_535,
Pongo abelii	ENSPPYG00000012683	2 retrocopies	retro_pabe_1789, retro_pabe_463,
Pan troglodytes	ENSPTRG00000011624	2 retrocopies	retro_ptro_1400, retro_ptro_157,
Pteropus vampyrus	ENSPVAG00000003660	1 retrocopy	retro_pvam_689,
Rattus norvegicus	ENSRNOG00000008950	1 retrocopy	retro_rnor_1316,
Tarsius syrichta	ENSTSYG00000004138	1 retrocopy	retro_tsyr_1271,
Tursiops truncatus	ENSTTRG00000005942	2 retrocopies	retro_ttru_1485, retro_ttru_1562,