RetrogeneDB ID: retro_pabe_2507

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:17387541..17387964(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NACA
• Ensembl ID: ENSPPYG00000004670
• Aliases: None
• Description: nascent polypeptide-associated complex subunit alpha [Source:RefSeq peptide;Acc:NP_001125923]

Sequence

>retro_pabe_2507
ATGCCTGGTGAAGCCACAGAAACCATTTTTGCTACAGAGCGGAAGTTGCCACAGCCCCAGGTGGAGACCGGGTCTGGAAC
AGAAGCTGACAGTGATAAATCAGTACCAGAGCTTGAGGAACAGGATTCCACAGAGACACCACACAATCAGCCCAGCTGGC
AGCAGTAGCTGAAATCAATGAGTGTCAATCGGTAAAGCAAAACAGAGTTAGAGTGAAAAGAAGGCACGTAAGGCTATGTC
CAAACTCGGTCTTCCATAGATAACAGGGGTTACTACAGTCACTACTGGAAATCTAAGAATATCTTCTTTGTCATCACAAA
ACCAGATGTCTACAAGAACCCTGCTTCAGATACCTATGTGTGTGTTTTTGGGGAAGCCAAGATCAAGGATTTATCTTAAC
AAGCATGGGTAGCACCTGCTGAG

Alignment

ORF - retro_pabe_2507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.86 %
• Parental protein coverage: 65.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPGEATETVPATEQELPQPQAETGSGTESDSDESVPELEEQDSTQA-TTQQAQLAAAAEIDE-EPVSKAK
          MPGEATET..ATE..LPQPQ.ETGSGTE.DSD.SVPELEEQDST...TTQ.AQLAA.AEI.E.....KAK
Retrocopy MPGEATETIFATERKLPQPQVETGSGTEADSDKSVPELEEQDSTET<TTQSAQLAAVAEINE<VSIGKAK

Parental  QSRSEKKARKAMSKLGLRQVTGVTRVTIR-KSKNILFVITKPDVYKSPASDTYI-VFGEAKIEDLSQQAQ
          QS.SEKKARKAMSKLGL...TGVT.VT...KSKNI.FVITKPDVYK.PASDTY..VFGEAKI.DLS.QA.
Retrocopy QS*SEKKARKAMSKLGLP*ITGVTTVTTG<KSKNIFFVITKPDVYKNPASDTYVCVFGEAKIKDLS*QAW

Parental  LAAAE
          .A.AE
Retrocopy VAPAE

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	96.54 RPM
SRP007412_cerebellum	0.00 RPM	158.81 RPM
SRP007412_heart	0.00 RPM	117.64 RPM
SRP007412_kidney	0.00 RPM	237.50 RPM
SRP007412_liver	0.00 RPM	217.52 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2507 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2507 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2507 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3027

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 81 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004175	3 retrocopies	retro_amel_1725, retro_amel_1821, retro_amel_643,
Bos taurus	ENSBTAG00000010701	2 retrocopies	retro_btau_1237, retro_btau_1620,
Canis familiaris	ENSCAFG00000000141	8 retrocopies	retro_cfam_1502, retro_cfam_1561, retro_cfam_1884, retro_cfam_1913, retro_cfam_2096, retro_cfam_2169, retro_cfam_710, retro_cfam_974,
Callithrix jacchus	ENSCJAG00000010701	8 retrocopies	retro_cjac_1063, retro_cjac_1452, retro_cjac_1875, retro_cjac_2202, retro_cjac_2453, retro_cjac_2696, retro_cjac_2975, retro_cjac_3232,
Dipodomys ordii	ENSDORG00000014522	2 retrocopies	retro_dord_228, retro_dord_699,
Erinaceus europaeus	ENSEEUG00000010458	5 retrocopies	retro_eeur_170, retro_eeur_207, retro_eeur_242, retro_eeur_334, retro_eeur_520,
Loxodonta africana	ENSLAFG00000004598	6 retrocopies	retro_lafr_1107, retro_lafr_113, retro_lafr_1251, retro_lafr_166, retro_lafr_491, retro_lafr_958,
Microcebus murinus	ENSMICG00000016465	5 retrocopies	retro_mmur_1122, retro_mmur_450, retro_mmur_585, retro_mmur_684, retro_mmur_807,
Myotis lucifugus	ENSMLUG00000001169	16 retrocopies	retro_mluc_1147, retro_mluc_1653, retro_mluc_1668, retro_mluc_1756, retro_mluc_1767, retro_mluc_1851, retro_mluc_1881, retro_mluc_1941, retro_mluc_2587, retro_mluc_2600, retro_mluc_414, retro_mluc_492, retro_mluc_526, retro_mluc_641, retro_mluc_725, retro_mluc_861,
Mus musculus	ENSMUSG00000061315	1 retrocopy	retro_mmus_968,
Nomascus leucogenys	ENSNLEG00000017449	7 retrocopies	retro_nleu_1358, retro_nleu_20, retro_nleu_2522, retro_nleu_478, retro_nleu_754, retro_nleu_839, retro_nleu_941,
Ochotona princeps	ENSOPRG00000001781	3 retrocopies	retro_opri_264, retro_opri_758, retro_opri_961,
Procavia capensis	ENSPCAG00000007067	5 retrocopies	retro_pcap_150, retro_pcap_224, retro_pcap_282, retro_pcap_305, retro_pcap_324,
Pongo abelii	ENSPPYG00000004670	6 retrocopies	retro_pabe_2507 , retro_pabe_26, retro_pabe_3279, retro_pabe_633, retro_pabe_656, retro_pabe_764,
Sarcophilus harrisii	ENSSHAG00000002175	1 retrocopy	retro_shar_213,
Ictidomys tridecemlineatus	ENSSTOG00000009028	1 retrocopy	retro_itri_367,
Vicugna pacos	ENSVPAG00000004028	2 retrocopies	retro_vpac_485, retro_vpac_611,