RetrogeneDB ID: retro_ogar_3320

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873777.1:224609..225031(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCNP
• Ensembl ID: ENSOGAG00000001821
• Aliases: None
• Description: PEST proteolytic signal containing nuclear protein [Source:HGNC Symbol;Acc:30023]

Sequence

>retro_ogar_3320
AGACAAGGAGGTGGGGAAGGCCACACAGGAGAAGCTTGAAAGGCTGTAGCAAGTCAGAGCCACCAGAGTAATGGGGTGGA
AATTCCAGTCACAGTGCTGAGAAGAGATCCACTGAAGAAGAAGCTACAGGCATCTCAACAAAGCCTATAAACATCACCTG
GTTTGGATTTGCCCCAGGTCATCACACAACAAAGAAAGCATCAAGCTTATCCACCAAACGTGCACCAAGTAACCCTAAAG
AAACGGCCCCAACCCTGGTTCCAAAGGCTCTTTCAGTAGCAGTGGCTTTTAATGAAGATGAAGATAGTGAAGCAGAGGAA
ATGCCTCCGGAAGCAAAGATGAAAATGAAGACTATGGGAAAGGATACACCAACATCAGCTGGACCAGACTTCTTCAAAAA
GCATAGGTTTTCTGATTCCCAG

Alignment

ORF - retro_ogar_3320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.69 %
• Parental protein coverage: 80.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RAGAAGGPEEEAEKPVKTKTVSSSNG-GESTSRSAEKRSAEEEAADLPTKPTKISKFGFAIGSQMTKKAS
          R.G...G...EA.K.V.......SNG.G...S.SAEKRS.EEEA....TKP..I..FGFA.G...TKKAS
Retrocopy RQGGGEGHTGEA*KAVASQS-HQSNG<GGNSSHSAEKRSTEEEATGISTKPINITWFGFAPGHHTTKKAS

Parental  AISIKLGSSKPKETVPTLAPKTLSVAAAFNEDEDSEPEEMPPEAKMRMKNIGRDTPTSAGPNSFNKGKHG
          ..S.K...S.PKET.PTL.PK.LSVA.AFNEDEDSE.EEMPPEAKM.MK..G.DTPTSAGP..F...KH.
Retrocopy SLSTKRAPSNPKETAPTLVPKALSVAVAFNEDEDSEAEEMPPEAKMKMKTMGKDTPTSAGPDFFK--KHR

Parental  FSDNQ
          FSD.Q
Retrocopy FSDSQ

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3320 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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.

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007972	11 retrocopies	retro_chof_1170, retro_chof_1215, retro_chof_2070, retro_chof_2280, retro_chof_2290, retro_chof_2553, retro_chof_2575, retro_chof_594, retro_chof_651, retro_chof_806, retro_chof_819,
Callithrix jacchus	ENSCJAG00000000508	6 retrocopies	retro_cjac_101, retro_cjac_1569, retro_cjac_1722, retro_cjac_3205, retro_cjac_3332, retro_cjac_401,
Cavia porcellus	ENSCPOG00000010610	2 retrocopies	retro_cpor_1335, retro_cpor_443,
Dasypus novemcinctus	ENSDNOG00000008873	5 retrocopies	retro_dnov_1606, retro_dnov_259, retro_dnov_370, retro_dnov_910, retro_dnov_98,
Gorilla gorilla	ENSGGOG00000025423	4 retrocopies	retro_ggor_882, retro_ggor_901, retro_ggor_902, retro_ggor_994,
Loxodonta africana	ENSLAFG00000005518	2 retrocopies	retro_lafr_1189, retro_lafr_458,
Macaca mulatta	ENSMMUG00000017782	3 retrocopies	retro_mmul_1312, retro_mmul_1377, retro_mmul_2598,
Mustela putorius furo	ENSMPUG00000011696	1 retrocopy	retro_mputfur_850,
Otolemur garnettii	ENSOGAG00000001821	4 retrocopies	retro_ogar_2216, retro_ogar_2465, retro_ogar_3320 , retro_ogar_652,
Procavia capensis	ENSPCAG00000007007	3 retrocopies	retro_pcap_161, retro_pcap_194, retro_pcap_273,