RetrogeneDB ID: retro_ptro_1347

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:9529131..9529545(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBXN2A
• Ensembl ID: ENSPTRG00000011705
• Aliases: UBXN2A, UBXD4
• Description: None

Sequence

>retro_ptro_1347
ACAAATTATGAATAGTTTGTTGATAGCCTTTTTGAGGAAGCTCAGAAGGTTGGTTCCAAATGCTTGTCTCCCACTTAACA
AAACAAACAGGTAGACGTAAACATAAAATTATGGAAAAATGGATTCACCGTCAACAATTATTTCAGAAGTTATTCAAATG
GTGCAAGTCAGCAGTTTCTGAACTCCATCAAAAAGGGGGAATTACCTTCAGAATTACAGGGAATTTTTGATAAAGAAGAG
GTGGGTGTTAAAGTTGAAGACAAGAAAAATGAAATATGTATGTCTACGAAGCCTGTCTTCCAGCTCTTTTCAGGACAGGG
TCACCAAGTAGGAAGGGTAAGCCATATCAAAGACTTCATTGAAAACTACCAAGGATCTCAAAAGAAGTCCTCCCCTGTCC
CTGGCAACAGTTTG

Alignment

ORF - retro_ptro_1347 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.29 %
• Parental protein coverage: 54.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SNCEYFVDSLFEEAQKVSSKCVSPAEQKKQVDVNIKLWKNGFTVNNDFRSYSDGASQQFLNSIKKGELPS
          .N.E.FVDSLFEEAQKV.SKC.SP..Q.KQVDVNIKLWKNGFTVNN.FRSYS.GASQQFLNSIKKGELPS
Retrocopy TNYE*FVDSLFEEAQKVGSKCLSPT*QNKQVDVNIKLWKNGFTVNNYFRSYSNGASQQFLNSIKKGELPS

Parental  ELQGIFDKEEVDVKVEDKKNEICLSTKPVFQPFSGQGHRLGSATPKIVSKAKNIEIENKNNLSAVPLNNL
          ELQGIFDKEEV.VKVEDKKNEIC.STKPVFQ.FSGQGH..G.....I.....N.....K...S.VP.N.L
Retrocopy ELQGIFDKEEVGVKVEDKKNEICMSTKPVFQLFSGQGHQVGRVS-HIKDFIENYQGSQKKS-SPVPGNSL

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	0.11 RPM	1.64 RPM
SRP007412_cerebellum	0.29 RPM	3.48 RPM
SRP007412_heart	0.09 RPM	6.09 RPM
SRP007412_kidney	0.13 RPM	3.69 RPM
SRP007412_liver	0.10 RPM	2.42 RPM
SRP007412_testis	0.63 RPM	3.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1347 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1347 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1347 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2025

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001640	5 retrocopies	retro_chof_1096, retro_chof_1171, retro_chof_2641, retro_chof_961, retro_chof_964,
Callithrix jacchus	ENSCJAG00000007665	1 retrocopy	retro_cjac_2085,
Equus caballus	ENSECAG00000020144	1 retrocopy	retro_ecab_569,
Echinops telfairi	ENSETEG00000002623	1 retrocopy	retro_etel_1116,
Homo sapiens	ENSG00000173960	1 retrocopy	retro_hsap_2025,
Gorilla gorilla	ENSGGOG00000002445	1 retrocopy	retro_ggor_1463,
Myotis lucifugus	ENSMLUG00000015640	1 retrocopy	retro_mluc_1195,
Macaca mulatta	ENSMMUG00000006487	1 retrocopy	retro_mmul_2068,
Mus musculus	ENSMUSG00000020634	1 retrocopy	retro_mmus_1007,
Nomascus leucogenys	ENSNLEG00000000751	1 retrocopy	retro_nleu_2612,
Oryctolagus cuniculus	ENSOCUG00000008783	1 retrocopy	retro_ocun_207,
Otolemur garnettii	ENSOGAG00000000025	1 retrocopy	retro_ogar_1909,
Procavia capensis	ENSPCAG00000011502	4 retrocopies	retro_pcap_169, retro_pcap_255, retro_pcap_271, retro_pcap_323,
Pan troglodytes	ENSPTRG00000011705	1 retrocopy	retro_ptro_1347 ,
Pan troglodytes	ENSPTRG00000013164	1 retrocopy	retro_ptro_2745,
Pan troglodytes	ENSPTRG00000033886	1 retrocopy	retro_ptro_2668,
Rattus norvegicus	ENSRNOG00000004950	2 retrocopies	retro_rnor_1746, retro_rnor_2966,
Sorex araneus	ENSSARG00000010108	1 retrocopy	retro_sara_272,
Sus scrofa	ENSSSCG00000026283	1 retrocopy	retro_sscr_537,
Tupaia belangeri	ENSTBEG00000012158	1 retrocopy	retro_tbel_3887,