RetrogeneDB ID: retro_pabe_485

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:202601863..202602222(-)
• Located in intron of: ENSPPYG00000001656

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNDC17
• Ensembl ID: ENSPPYG00000007880
• Aliases: None
• Description: Thioredoxin domain-containing protein 17 [Source:UniProtKB/Swiss-Prot;Acc:Q5REA8]

Sequence

>retro_pabe_485
TACAAGGAGGTGAGTGTGTGAAGCTTTGAGGAGTTCATCTGGGCTGTGGTACGCCACAATGGCAAGACCATTTTCACCTA
CTTTATCAGTTCTAAGGATGCTGGAGGAAAAGCTGGTGCCCCTATTGTATGCATGCCGAACCAGTCGTACGAAAGGGGCT
GAAGCATGTTAGTGAAGGATGTGTGTTCGCCTACTGCCAAGTAGAAGAAAAGCCTTATTGGAAAGATCCAAATAATGACT
TCAGAAAAAACTTGGAAGTAACCACAGTGCCTATACTACTTAAATATGGAACACCTCAAAAACTGGTAGAATCTTAGTGT
CTTCAGGCCAACCTCGTGGAAATGTTTTTCTCTAAGGAT

Alignment

ORF - retro_pabe_485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.34 %
• Parental protein coverage: 97.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YEEVSVSGFEEFHRAVEQHNGKTIFAYFTGSKDAGGK-SWCPDCVQAEPVVREGLKHISEGCVFIYCQVG
          Y.EVSV..FEEF..AV..HNGKTIF.YF..SKDAGGK.SWCP.C..AEPVVR.GLKH.SEGCVF.YCQV.
Retrocopy YKEVSV*SFEEFIWAVVRHNGKTIFTYFISSKDAGGK<SWCPYCMHAEPVVRKGLKHVSEGCVFAYCQVE

Parental  EKPYWKDPNNDFRKNLKVTAVPTLIKYGTPQKLVESECLQANLVEMLFSED
          EKPYWKDPNNDFRKNL.VT.VP.L.KYGTPQKLVES.CLQANLVEM.FS.D
Retrocopy EKPYWKDPNNDFRKNLEVTTVPILLKYGTPQKLVES*CLQANLVEMFFSKD

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	0.17 RPM	3.76 RPM
SRP007412_cerebellum	0.24 RPM	3.28 RPM
SRP007412_heart	0.03 RPM	4.76 RPM
SRP007412_kidney	0.13 RPM	38.68 RPM
SRP007412_liver	0.09 RPM	22.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_485 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_485 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_485 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_132
Pan troglodytes	retro_ptro_137
Gorilla gorilla	retro_ggor_230
Macaca mulatta	retro_mmul_365
Callithrix jacchus	retro_cjac_2887

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007038	4 retrocopies	retro_amel_1181, retro_amel_1267, retro_amel_148, retro_amel_344,
Callithrix jacchus	ENSCJAG00000011150	4 retrocopies	retro_cjac_2775, retro_cjac_2877, retro_cjac_2887, retro_cjac_3048,
Cavia porcellus	ENSCPOG00000002887	1 retrocopy	retro_cpor_116,
Equus caballus	ENSECAG00000025006	1 retrocopy	retro_ecab_430,
Echinops telfairi	ENSETEG00000001905	1 retrocopy	retro_etel_14,
Felis catus	ENSFCAG00000024143	1 retrocopy	retro_fcat_1128,
Homo sapiens	ENSG00000129235	2 retrocopies	retro_hsap_132, retro_hsap_2218,
Gorilla gorilla	ENSGGOG00000003055	2 retrocopies	retro_ggor_1750, retro_ggor_230,
Macropus eugenii	ENSMEUG00000008946	1 retrocopy	retro_meug_1771,
Microcebus murinus	ENSMICG00000006620	2 retrocopies	retro_mmur_1093, retro_mmur_766,
Macaca mulatta	ENSMMUG00000003788	2 retrocopies	retro_mmul_365, retro_mmul_932,
Mustela putorius furo	ENSMPUG00000011338	2 retrocopies	retro_mputfur_518, retro_mputfur_564,
Mus musculus	ENSMUSG00000020803	3 retrocopies	retro_mmus_2817, retro_mmus_2818, retro_mmus_488,
Nomascus leucogenys	ENSNLEG00000009230	2 retrocopies	retro_nleu_2262, retro_nleu_2516,
Oryctolagus cuniculus	ENSOCUG00000016557	1 retrocopy	retro_ocun_297,
Ochotona princeps	ENSOPRG00000000509	2 retrocopies	retro_opri_575, retro_opri_8,
Procavia capensis	ENSPCAG00000003749	1 retrocopy	retro_pcap_180,
Pongo abelii	ENSPPYG00000007880	1 retrocopy	retro_pabe_485 ,
Pan troglodytes	ENSPTRG00000008644	2 retrocopies	retro_ptro_137, retro_ptro_1683,
Pteropus vampyrus	ENSPVAG00000002399	1 retrocopy	retro_pvam_1187,
Rattus norvegicus	ENSRNOG00000014072	1 retrocopy	retro_rnor_1700,
Sorex araneus	ENSSARG00000006501	1 retrocopy	retro_sara_20,
Ictidomys tridecemlineatus	ENSSTOG00000021986	2 retrocopies	retro_itri_197, retro_itri_574,
Tupaia belangeri	ENSTBEG00000000539	1 retrocopy	retro_tbel_3760,
Tarsius syrichta	ENSTSYG00000010996	2 retrocopies	retro_tsyr_1058, retro_tsyr_982,
Tursiops truncatus	ENSTTRG00000012072	1 retrocopy	retro_ttru_1252,
Vicugna pacos	ENSVPAG00000001554	1 retrocopy	retro_vpac_501,