RetrogeneDB ID: retro_ogar_3213

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873742.1:165302..166188(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD14
• Ensembl ID: ENSOGAG00000004933
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 14 [Source:HGNC Symbol;Acc:16889]

Sequence

>retro_ogar_3213
TTGGGCCAGGGGCCACCTACAGATGCTTCTGTCATGGACACAGCAAAATAAGTCTATATCTCTTCTCTGGCACTGTTAAA
AATGTTAAAACATGGCCATGCTGGAATTCCAATGGAAGTTATGGATCTGATCCTTGGAGAATTTGTTGATGATTACACGG
TCAGAGTGATTGATGTGTTTGCCATGCCACAGTCAGGAACAGGTGTCAGTGTGGAGACAGTTGATCCAGTGTTCCAAGCC
AAGATGTTAGATATAGTGAAGCAGACAGGGAGGCCTGAGATGGTTGTTGGTTGGTATCACAGTCACCCTGGCTTTGGTTG
TTGGCTTTCAGGTATGGATATCAACACTCAGTAGAGCTTTGAAGCCTTCTGGAAGAGAGCTGTGGCAGTGGTTGTGGATC
CTATTCAGAATGTAAAAGGAAAGGTTGTTATTGAGGCCTTCAGATTGAGCAATGCTAATATGATGGTCTTAGGACATGAA
CCAAGACAAACAACTTCAAATCTGGGTCACTTAAACAAACCATCTATTCAGCCATTAATTCATAAATTAAAGACATTATT
ACTCCATTACTATTAACTATTGAAAAAATAAACTGGAACAGAAGATATTGATAAATTTACACAAGAAGAATTGGATGGAA
AGTTTAACACTTCAGGACTACAGTGAACATTGTAAACACAATGAATCAGTGGTAAAAGAGATGTTGGACTCAGCCAAGAA
TTATAATAAGGCTGTAGAAGAAGATAAGATGACACCTGAACAGATGGCAATAAAGAATGTTGGCAAGCAGGACCCCAAAC
ATCATTTGGAGGAACATATGGATGTACTTAAGACTTCAAATATTGTCCAGTGTTTAGTAGCTATGTTGGATACTGTCGTA
TTTAAA

Alignment

ORF - retro_ogar_3213 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.91 %
• Parental protein coverage: 96.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGEGPPTDAPAVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVRVIDVFAMPQSGTGVS
          LG.GPPTDA...DTA..VYISSLALLKMLKHG.AG.PMEVM.L.LGEFVDDYTVRVIDVFAMPQSGTGVS
Retrocopy LGQGPPTDASVMDTAK*VYISSLALLKMLKHGHAGIPMEVMDLILGEFVDDYTVRVIDVFAMPQSGTGVS

Parental  VEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSVKG
          VE.VDPVFQAKMLD..KQTGRPEMVVGWYHSHPGFGCWLSG.DINTQ.SFEA...RAVAVVVDPIQ.VKG
Retrocopy VETVDPVFQAKMLDIVKQTGRPEMVVGWYHSHPGFGCWLSGMDINTQ*SFEAFWKRAVAVVVDPIQNVKG

Parental  KVVIDAFRLINANMMVLGHEPRQTTSNLGHLNKPSIQALIHGL-NRHYYSITINYRKNELEQKMLLNLHK
          KVVI.AFRL.NANMMVLGHEPRQTTSNLGHLNKPSIQ.LIH.L....Y.SITINY.KN.LEQK.L.NLHK
Retrocopy KVVIEAFRLSNANMMVLGHEPRQTTSNLGHLNKPSIQPLIHKL>RHYY-SITINY*KNKLEQKILINLHK

Parental  KSWMEGLTLQDYSEHCKHNESVVKEMLELAKNYNKAVEEEDKMTPEQLAIKNVGKQDPKRHLEEHVDVLM
          K.WME.LTLQDYSEHCKHNESVVKEML..AKNYNKAV.EEDKMTPEQ.AIKNVGKQDPK.HLEEH.DVL.
Retrocopy KNWMESLTLQDYSEHCKHNESVVKEMLDSAKNYNKAV-EEDKMTPEQMAIKNVGKQDPKHHLEEHMDVLK

Parental  TSNIVQCLAAMLDTVVFK
          TSNIVQCL.AMLDTVVFK
Retrocopy TSNIVQCLVAMLDTVVFK

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_3213 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002556	1 retrocopy	retro_chof_2387,
Callithrix jacchus	ENSCJAG00000005572	1 retrocopy	retro_cjac_1434,
Gorilla gorilla	ENSGGOG00000015747	1 retrocopy	retro_ggor_1710,
Mus musculus	ENSMUSG00000026914	1 retrocopy	retro_mmus_701,
Otolemur garnettii	ENSOGAG00000004933	2 retrocopies	retro_ogar_2955, retro_ogar_3213 ,
Pongo abelii	ENSPPYG00000012881	1 retrocopy	retro_pabe_2100,
Pan troglodytes	ENSPTRG00000012575	1 retrocopy	retro_ptro_1636,
Rattus norvegicus	ENSRNOG00000004911	1 retrocopy	retro_rnor_1271,
Tupaia belangeri	ENSTBEG00000014118	1 retrocopy	retro_tbel_3917,