RetrogeneDB ID: retro_pabe_1980

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:19909264..19909926(-)
• Located in intron of: ENSPPYG00000012162

Retrocopy information

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

Parental gene information

• Parental gene symbol: C14orf166
• Ensembl ID: ENSPPYG00000005814
• Aliases: None
• Description: UPF0568 protein C14orf166 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q5R8I2]

Sequence

>retro_pabe_1980
CAATTTAGAAACTTCACTGTTTGGCTTGAAGAAAAGAAAATCAGACACTACAAGATTGAAGACAGAGGTAATTTAAGAAA
CATCCACAGCAGTGACTGGCCCAAGTTCTTTGAAAAGTATCTCAGAGATGTTAACTGTCCTTTAAAGATTCAAGATCGAC
AAGAAGCTATTGACTGGCTTCTTGGTTTAGCTGTTAGATTTGAATATGGAGATAACGCTGAAAAATACAAGGACTTAGTA
CCTGATAATGCAAAAACTGCTGACAATGCAACTAAAAATGCAGAACCATTGATACATTTTGACGTAAATAATCCTGATTT
TAAGTCTGGTGTAATGGCTTTGGCTAACCTGCTTCAGGTTCAACGTCATGATGATTGCCTGGTAATGCTTAAGGCAATTC
AAATTTTGGTTCAGGAGCGCCTGACACAGGATGCAGTTGCTAAAGCAAATCAAACAAAAGAGGGCTAGCCTGTTGCTTTA
GACAAACATATTCTTGGTTTTGACACAGGAGATGCAGTTCTTAATGAAGCTACTCAAATCTGCGATTGCTGCATACAGAA
GAGCTCAGACAGCTACAGACAAAAATTAATGAAGCCACAGTAGCTGTTCAGGCAATTATTGCTGATGCAAGGACAGACCA
CAGGCTGGGAAAAGTTGGAAGA

Alignment

ORF - retro_pabe_1980 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.54 %
• Parental protein coverage: 90.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EFRNFIVWLEDQKIRHYKIEDRGNLRNIHSSDWPKFFEKYLRDVNCPFKIQDRQEAIDWLLGLAVRLEYG
          .FRNF.VWLE..KIRHYKIEDRGNLRNIHSSDWPKFFEKYLRDVNCP.KIQDRQEAIDWLLGLAVR.EYG
Retrocopy QFRNFTVWLEEKKIRHYKIEDRGNLRNIHSSDWPKFFEKYLRDVNCPLKIQDRQEAIDWLLGLAVRFEYG

Parental  DNAEKYKDLVPDNSKTADNATKNAEPLINLDVNNPDFKAGVMALANLLQIQRHDDYLVMLKAIRILVQER
          DNAEKYKDLVPDN.KTADNATKNAEPLI..DVNNPDFK.GVMALANLLQ.QRHDD.LVMLKAI.ILVQER
Retrocopy DNAEKYKDLVPDNAKTADNATKNAEPLIHFDVNNPDFKSGVMALANLLQVQRHDDCLVMLKAIQILVQER

Parental  LTQDAVAKANQTKEGLPVALDKHILGFDTGDAVLNEAAQI-LRLLHIEELRELQTKINEAIVAVQAIIAD
          LTQDAVAKANQTKEG.PVALDKHILGFDTGDAVLNEA.QI.LRLLH.EELR.LQTKINEA.VAVQAIIAD
Retrocopy LTQDAVAKANQTKEG*PVALDKHILGFDTGDAVLNEATQI<LRLLHTEELRQLQTKINEATVAVQAIIAD

Parental  PKTDHRLGKVGR
          ..TDHRLGKVGR
Retrocopy ARTDHRLGKVGR

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	0.06 RPM	24.05 RPM
SRP007412_cerebellum	0.00 RPM	42.68 RPM
SRP007412_heart	0.03 RPM	78.60 RPM
SRP007412_kidney	0.10 RPM	42.63 RPM
SRP007412_liver	0.12 RPM	43.94 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1980 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1980 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1980 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2307
Pan troglodytes	retro_ptro_1631

---

Parental genes homology:

Parental genes homology involve 29 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002083	2 retrocopies	retro_amel_224, retro_amel_302,
Canis familiaris	ENSCAFG00000014648	4 retrocopies	retro_cfam_1025, retro_cfam_2042, retro_cfam_237, retro_cfam_734,
Callithrix jacchus	ENSCJAG00000006926	3 retrocopies	retro_cjac_1262, retro_cjac_1947, retro_cjac_3207,
Cavia porcellus	ENSCPOG00000001317	6 retrocopies	retro_cpor_1041, retro_cpor_1177, retro_cpor_1239, retro_cpor_1247, retro_cpor_517, retro_cpor_541,
Dasypus novemcinctus	ENSDNOG00000003248	3 retrocopies	retro_dnov_458, retro_dnov_572, retro_dnov_609,
Dipodomys ordii	ENSDORG00000012335	1 retrocopy	retro_dord_619,
Equus caballus	ENSECAG00000012600	1 retrocopy	retro_ecab_483,
Erinaceus europaeus	ENSEEUG00000015583	1 retrocopy	retro_eeur_366,
Felis catus	ENSFCAG00000002663	3 retrocopies	retro_fcat_1160, retro_fcat_1415, retro_fcat_948,
Homo sapiens	ENSG00000087302	1 retrocopy	retro_hsap_2307,
Loxodonta africana	ENSLAFG00000003162	1 retrocopy	retro_lafr_301,
Microcebus murinus	ENSMICG00000008720	1 retrocopy	retro_mmur_857,
Myotis lucifugus	ENSMLUG00000008643	6 retrocopies	retro_mluc_1228, retro_mluc_1518, retro_mluc_1834, retro_mluc_2610, retro_mluc_456, retro_mluc_676,
Macaca mulatta	ENSMMUG00000018200	2 retrocopies	retro_mmul_1045, retro_mmul_2025,
Monodelphis domestica	ENSMODG00000013211	1 retrocopy	retro_mdom_1296,
Mustela putorius furo	ENSMPUG00000005253	6 retrocopies	retro_mputfur_1333, retro_mputfur_1421, retro_mputfur_203, retro_mputfur_328, retro_mputfur_655, retro_mputfur_797,
Mus musculus	ENSMUSG00000021807	2 retrocopies	retro_mmus_140, retro_mmus_3203,
Nomascus leucogenys	ENSNLEG00000012406	1 retrocopy	retro_nleu_2749,
Oryctolagus cuniculus	ENSOCUG00000014681	1 retrocopy	retro_ocun_221,
Otolemur garnettii	ENSOGAG00000013232	5 retrocopies	retro_ogar_1060, retro_ogar_1856, retro_ogar_2351, retro_ogar_2976, retro_ogar_3192,
Ochotona princeps	ENSOPRG00000016352	2 retrocopies	retro_opri_257, retro_opri_884,
Pongo abelii	ENSPPYG00000005814	1 retrocopy	retro_pabe_1980 ,
Pan troglodytes	ENSPTRG00000006344	1 retrocopy	retro_ptro_1631,
Pteropus vampyrus	ENSPVAG00000013392	1 retrocopy	retro_pvam_1088,
Sus scrofa	ENSSSCG00000005029	1 retrocopy	retro_sscr_1093,
Tupaia belangeri	ENSTBEG00000013898	5 retrocopies	retro_tbel_2579, retro_tbel_4337, retro_tbel_683, retro_tbel_880, retro_tbel_881,
Tarsius syrichta	ENSTSYG00000004528	6 retrocopies	retro_tsyr_1183, retro_tsyr_1289, retro_tsyr_1353, retro_tsyr_157, retro_tsyr_541, retro_tsyr_939,
Tursiops truncatus	ENSTTRG00000005721	1 retrocopy	retro_ttru_83,
Vicugna pacos	ENSVPAG00000011443	1 retrocopy	retro_vpac_142,