RetrogeneDB ID: retro_opri_961

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_5050:120..589(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NACA2
• Ensembl ID: ENSOPRG00000001781
• Aliases: None
• Description: nascent polypeptide-associated complex alpha subunit 2 [Source:HGNC Symbol;Acc:23290]

Sequence

>retro_opri_961
CTGGCCGCAGCAGCTGAACTGATGGAGAACCATCAATAAGGCAAAACAGAGTGAGTGTGAGAAGAAGGCACCGAAGGCTA
TGTCCAAGCTGGGTCTTCAGCAGGTTACAGGGGTTGTAGAGTCACTTTCTGGAAATCTAAGACTATCGTCTTTGTCATCA
CAAAACCAGATGTCTACAAGAGCCCAGCCTCAGACACGTCCTTTGCTTTTGGGGAAGCCAAGACTGAGGATTTATCTCAG
CAAGCACAGCTGGCAGCAGCTGAGGGATTCAAAGTTCAAGGTGAAGCTGTCTCCAACATTCAGGCAAATACACAGACTCC
CACTCTACAGGTGGAGAGTAAAGAGGAAAAGGTTAATGAAGCAGGTGTGGAAGTTAGGATATAGAGTTGGTTACATCACA
AACAAATGTGTCCAGAGCAAAGACAGTTGAGCCCCGAAGAACAGCAGTAATGCGTTTGTAAATTCTATT

Alignment

ORF - retro_opri_961 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.46 %
• Parental protein coverage: 73.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LAAAAEI-DEEP-VSKAKQSRSEKKARKAMSKLGLRQVTGVT-RVTIRKSKNILFVITKPDVYKSPASDT
          LAAAAE..D.EP...KAKQS..EKKA.KAMSKLGL.QVTGV..RVT..KSK.I.FVITKPDVYKSPASDT
Retrocopy LAAAAEL<DGEP<INKAKQSECEKKAPKAMSKLGLQQVTGVV<RVTFWKSKTIVFVITKPDVYKSPASDT

Parental  YIVFGEAKIEDLSQQAQLAAAEKFKVQGEAVSNIQENTQTPTVQEESEEEEVDETGVEVK-DIELVMSQA
          ...FGEAK.EDLSQQAQLAAAE.FKVQGEAVSNIQ.NTQTPT.Q.ES.EE.V.E.GVEV..DIELV.SQ.
Retrocopy SFAFGEAKTEDLSQQAQLAAAEGFKVQGEAVSNIQANTQTPTLQVESKEEKVNEAGVEVR<DIELVTSQT

Parental  NVSRAKAVR-ALKNNSNDIVNAI
          NVSRAK.V..A.KN.SN..VN.I
Retrocopy NVSRAKTVE<APKNSSNAFVNSI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_961 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 14 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,
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,
Homo sapiens	ENSG00000196531	6 retrocopies	retro_hsap_3006, retro_hsap_3027, retro_hsap_3968, retro_hsap_3992, retro_hsap_737, retro_hsap_77,
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,
Macaca mulatta	ENSMMUG00000003073	4 retrocopies	retro_mmul_1233, retro_mmul_1933, retro_mmul_2066, retro_mmul_889,
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,
Vicugna pacos	ENSVPAG00000004028	2 retrocopies	retro_vpac_485, retro_vpac_611,