RetrogeneDB ID: retro_hsap_917

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:93731808..93732392(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000256752
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HPRT1
• Ensembl ID: ENSG00000165704
• Aliases: HPRT1, HGPRT, HPRT
• Description: hypoxanthine phosphoribosyltransferase 1 [Source:HGNC Symbol;Acc:5157]

Sequence

>retro_hsap_917
ATTGTTACCCACAGCCCCAGCATCATGATTAGTGATGATGAACCAGGTTATAACCTAGATTTATATCATATACCTCATCA
TTACACTGAGGATTTGCAAAAGGTTTTATTCCTCATGGACTGATTGTGAACAGGACCAAACGACTTGCCTGAGATGTGAT
GAAGGAGATAGGAGCCTCTCACATTGTAGCCTTCTGTTTGTTCAAGGGGGGTTGTACTTTTTTTGCTGACCTGCTAGATA
ACATCAAAGCACCTGAATAGAAATAGTCATAGAGCCATTCCTATGATAGAGCCAATACAGAGCAAGGAGCTACTGTAATG
ACCAGTCAACAGGGGATATAAAGGTAATTGGTGGCGATGATCCTTCAACTTTAACTAGAAAGAATGTCTTGATTTTTGAA
GATGTAATTGACACTGGCAAAACAATGCCAACCTTGCCTTCTGGGTCAAGTACTATAATCTAAAAATGGTCAAGGTTTGC
AAGCTCGCTAGTGAGAAAGCACCCTTCAGAGTGTTAGAAATAGGCCAGACTTTGTTGGATTTGAAATTCCAGACAAACTT
GTTGCAGGATATGCCCTTTTCTAT

Alignment

ORF - retro_hsap_917 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.65 %
• Parental protein coverage: 89.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MATRSPGVVISDDEPGYDLDLFCIPNHYAEDLERV-FIPHGLIMDRTERLARDVMKEMGGHHIVALCVLK
          ..T.SP...ISDDEPGY.LDL..IP.HY.EDL..V.FIPHGLI..RT.RLA.DVMKE.G..HIVA.C..K
Retrocopy IVTHSPSIMISDDEPGYNLDLYHIPHHYTEDLQKV<FIPHGLIVNRTKRLA*DVMKEIGASHIVAFCLFK

Parental  GGYKFFADLLDYIKA-LNRNSDRSIPMTVDFIRLK-SYCNDQSTGDIKVIGGDDLSTLTGKNVLIVEDII
          GG..FFADLLD.IKA.LNRNS.R.IPM....I..K.SYCNDQSTGDIKVIGGDD.STLT.KNVLI.ED.I
Retrocopy GGCTFFADLLDNIKA>LNRNSHRAIPM-IEPIQSK>SYCNDQSTGDIKVIGGDDPSTLTRKNVLIFEDVI

Parental  DTGKTMQTLLS-LVRQYNPKMVKV-ASLLVKRTP-RSVGYKPDFVGFEIPDKFVVGYALDY
          DTGKTM.TL.S..V..YN.KMVKV.AS.LV...P..SV...PDFVGFEIPDK.V.GYAL.Y
Retrocopy DTGKTMPTLPS<WVKYYNLKMVKV>ASSLVRKHP>QSVRNRPDFVGFEIPDKLVAGYALFY

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	19.24 RPM
bodymap2_adrenal	0.00 RPM	28.31 RPM
bodymap2_brain	0.00 RPM	91.79 RPM
bodymap2_breast	0.00 RPM	15.76 RPM
bodymap2_colon	0.00 RPM	22.93 RPM
bodymap2_heart	0.00 RPM	13.66 RPM
bodymap2_kidney	0.00 RPM	55.69 RPM
bodymap2_liver	0.00 RPM	11.30 RPM
bodymap2_lung	0.00 RPM	31.45 RPM
bodymap2_lymph_node	0.00 RPM	19.48 RPM
bodymap2_ovary	0.00 RPM	41.12 RPM
bodymap2_prostate	0.00 RPM	22.05 RPM
bodymap2_skeletal_muscle	0.00 RPM	16.10 RPM
bodymap2_testis	0.00 RPM	90.59 RPM
bodymap2_thyroid	0.00 RPM	36.36 RPM
bodymap2_white_blood_cells	0.00 RPM	32.27 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_917 was not detected

EST

No EST(s) were mapped for retro_hsap_917 retrocopy.

TSS

No TSS is located nearby retro_hsap_917 retrocopy 5' end.

Lab

retro_hsap_917 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_917 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_636
Gorilla gorilla	retro_ggor_740

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001339	1 retrocopy	retro_amel_129,
Bos taurus	ENSBTAG00000014685	3 retrocopies	retro_btau_162, retro_btau_179, retro_btau_721,
Canis familiaris	ENSCAFG00000018870	1 retrocopy	retro_cfam_2014,
Cavia porcellus	ENSCPOG00000002512	1 retrocopy	retro_cpor_1299,
Dasypus novemcinctus	ENSDNOG00000008495	5 retrocopies	retro_dnov_1480, retro_dnov_1908, retro_dnov_2057, retro_dnov_255, retro_dnov_763,
Equus caballus	ENSECAG00000017534	1 retrocopy	retro_ecab_734,
Felis catus	ENSFCAG00000004575	2 retrocopies	retro_fcat_104, retro_fcat_1608,
Homo sapiens	ENSG00000165704	1 retrocopy	retro_hsap_917 ,
Gorilla gorilla	ENSGGOG00000008050	1 retrocopy	retro_ggor_740,
Loxodonta africana	ENSLAFG00000009892	2 retrocopies	retro_lafr_1042, retro_lafr_475,
Microcebus murinus	ENSMICG00000006547	1 retrocopy	retro_mmur_1186,
Myotis lucifugus	ENSMLUG00000003591	1 retrocopy	retro_mluc_2107,
Macaca mulatta	ENSMMUG00000008303	1 retrocopy	retro_mmul_1118,
Mustela putorius furo	ENSMPUG00000012699	3 retrocopies	retro_mputfur_1317, retro_mputfur_1638, retro_mputfur_836,
Oryctolagus cuniculus	ENSOCUG00000003186	1 retrocopy	retro_ocun_1082,
Otolemur garnettii	ENSOGAG00000003881	3 retrocopies	retro_ogar_1886, retro_ogar_3298, retro_ogar_3463,
Pongo abelii	ENSPPYG00000020733	2 retrocopies	retro_pabe_3601, retro_pabe_791,
Pan troglodytes	ENSPTRG00000022287	2 retrocopies	retro_ptro_2042, retro_ptro_636,
Rattus norvegicus	ENSRNOG00000031367	2 retrocopies	retro_rnor_1208, retro_rnor_2491,
Sarcophilus harrisii	ENSSHAG00000007965	3 retrocopies	retro_shar_470, retro_shar_513, retro_shar_661,
Tupaia belangeri	ENSTBEG00000000859	5 retrocopies	retro_tbel_1607, retro_tbel_2234, retro_tbel_3627, retro_tbel_4320, retro_tbel_729,
Tarsius syrichta	ENSTSYG00000009579	1 retrocopy	retro_tsyr_2050,
Tursiops truncatus	ENSTTRG00000009954	9 retrocopies	retro_ttru_1007, retro_ttru_1272, retro_ttru_1523, retro_ttru_1598, retro_ttru_1620, retro_ttru_276, retro_ttru_641, retro_ttru_732, retro_ttru_829,
Vicugna pacos	ENSVPAG00000009133	1 retrocopy	retro_vpac_122,