RetrogeneDB ID: retro_pabe_3601

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:57864542..57864982(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: HPRT1
• Ensembl ID: ENSPPYG00000020733
• Aliases: None
• Description: hypoxanthine phosphoribosyltransferase 1 [Source:HGNC Symbol;Acc:5157]

Sequence

>retro_pabe_3601
ATTGTTACCCACAGCCCCAGCATCATGATTAGTGATGATGAACCAGGTTATGACCTAGATTTATATCATATACCTCATCA
TTACACTGAAGATTTGCAAAAGGTTTTATTCCTCATGGACTGATTGTGAACAGGACCAAACGACTTGCCTGAGATGTGAT
GAAAGAGATAGGAGCTCTCACATTGTAGCCTTCTGTTTGATCAAAGGGGGCTGTATGTTTTTTGCTGACCTACTAGATAA
CATCAAAGTACCTGAATAGAAATAGTCATAGAGCCATTCCTATGATAGAGCCAATAAAGAGCAAGGAGCTACTGTAATGA
CCAGTCAACAGGGGACATAAAGGTAATTGGTGGTGATGATCTTTCAACTTTAACTAGAAAGAATGTCTTGATTTTTGAAG
ATGTATTGACACTGGCAAAACAATGCAAACCTTGCCTTCT

Alignment

ORF - retro_pabe_3601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.9 %
• Parental protein coverage: 67.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MATRSPGVVISDDEPGYDLDLFCIPNHYAEDLERV-FIPHGLIMDRTERLARDVMKEMG-GHHIVALCVL
          ..T.SP...ISDDEPGYDLDL..IP.HY.EDL..V.FIPHGLI..RT.RLA.DVMKE.G...HIVA.C..
Retrocopy IVTHSPSIMISDDEPGYDLDLYHIPHHYTEDLQKV<FIPHGLIVNRTKRLA*DVMKEIG<SSHIVAFCLI

Parental  KGGYKFFADLLDYIKA-LNRNSDRSIPMTVDFIRLK-SYCNDQSTGDIKVIGGDDLSTLTGKNVLIVEDI
          KGG..FFADLLD.IK..LNRNS.R.IPM....I..K.SYCNDQSTGDIKVIGGDDLSTLT.KNVLI.ED.
Retrocopy KGGCMFFADLLDNIKV>LNRNSHRAIPM-IEPIKSK>SYCNDQSTGDIKVIGGDDLSTLTRKNVLIFEDV

Parental  -IDTGKTMQTLLS
          .IDTGKTMQTL.S
Retrocopy <IDTGKTMQTLPS

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	31.96 RPM
SRP007412_cerebellum	0.00 RPM	43.53 RPM
SRP007412_heart	0.00 RPM	9.36 RPM
SRP007412_kidney	0.00 RPM	10.77 RPM
SRP007412_liver	0.00 RPM	8.38 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3601 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3601 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3601 has 0 orthologous retrocopies within eutheria group .

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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,