RetrogeneDB ID: retro_ogar_3137

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873727.1:1617108..1617663(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA5
• Ensembl ID: ENSOGAG00000013560
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 5 [Source:HGNC Symbol;Acc:9534]

Sequence

>retro_ogar_3137
CAGAAGAGAATTATCTCCCCACCAATGGAGCCCAGCAACACTGGTGAGATTGTAGAGATTGATGACCACATACCTTGTGC
GATGAGTGGGCTAAATGCTAAGACTTTAATTGATAAAGGCAGGGTGAAGACATGGAACTATTGGTTCAGTTGTAGTGAAA
CAATGATGGTGGACAGTGTGACCCAGGATGTGCCCAACTGGCTTTGCAGTTTGGAGAGGAAGATGCACAGCCAGGTGCCA
TGTCTCATCTCCCTGGGGTAGCGCTGTTATTTGGAAGAGTTGAATGGAAAGGACCCCAGCTCTTTCACTGGGACCCTTCT
GGGATCCGTATTCTGTATGCACCAGCAAATTGACTATGCTTCAGAGGGTGCCCAGAGCTCCTTGCAAAAAGTTTAGTACA
AGTCTATGATTCTGAAAGAATCCATCAAGTCTTCCTTCATCACCCTTAGACAAGTAATGGAAGAGAAGCTGAACTCAGTG
CTAGCCACAGTACAGTGTGGCCAGAATTTCCACATGCTCACAAAGGAGCGGCCTGAGGAGGTTAGCAAGGACATT

Alignment

ORF - retro_ogar_3137 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.28 %
• Parental protein coverage: 79.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKRITSPLMEPSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSN-L
          .KRI.SP.MEPS....IVEID.HI.CAMSGL...AKTLIDK.RV.T.N.WF...ETM.V.SVTQ.V.N.L
Retrocopy QKRIISPPMEPSNTGEIVEIDDHIPCAMSGL--NAKTLIDKGRVKTWNYWFSCSETMMVDSVTQDVPN<L

Parental  ALQFGEEDADPGAMSRPFGVALLFGGVD-EKGPQLFHMDPSGTFVQCDARAIGSASEGAQSSLQEVYHKS
          ALQFGEEDA.PGAMS...GVALLFG.V...K.P..F.....G..V.C....I..ASEGAQSSLQ.V..KS
Retrocopy ALQFGEEDAQPGAMSHLPGVALLFGRVE>GKDPSSFTGTLLGS-VFCMHQQIDYASEGAQSSLQKV*YKS

Parental  MTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKDI
          M.LKE.IKSS.I.L.QVMEEKLN.....LATVQ.GQNFHM.TKE..EEV.KDI
Retrocopy MILKESIKSSFITLRQVMEEKLNSV---LATVQCGQNFHMLTKERPEEVSKDI

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_3137 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000008497	2 retrocopies	retro_mluc_1002, retro_mluc_926,
Mustela putorius furo	ENSMPUG00000003189	1 retrocopy	retro_mputfur_1295,
Mus musculus	ENSMUSG00000068749	1 retrocopy	retro_mmus_52,
Otolemur garnettii	ENSOGAG00000013560	1 retrocopy	retro_ogar_3137 ,
Pteropus vampyrus	ENSPVAG00000008908	1 retrocopy	retro_pvam_222,
Sus scrofa	ENSSSCG00000006830	2 retrocopies	retro_sscr_1156, retro_sscr_1194,