RetrogeneDB ID: retro_ogar_1147

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873537.1:7243702..7244153(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCL3
• Ensembl ID: ENSOGAG00000015138
• Aliases: None
• Description: phosducin-like 3 [Source:HGNC Symbol;Acc:28860]

Sequence

>retro_ogar_1147
GACCCCAATGCAGACACTAAGTGGAATGCCATCTTATGCAAAAAGGGCATCTTGCCCTTGAAGGAAACTCTGAGCGAATT
GAAAAAAGAAAAAGTCAGAAAAGGAGGAGCAGAGAGTCCTCCAGCACGTGGAGGTGAAACATGAAGCTAGGACTTGGGAA
GAGCTGGAAAGTCATGAAGATGAATTTGAAGAAGAGGATGAATGCACTATTGAAATGTACATGCAGCAAAGCCTGGCTGA
GTGGAAAGCAACTGAACTGGAAAATAAGTGTTCCATTTTGCACATCTCAGGAAAGAATTATGTTCAAGAAGTTACCAAAG
CCAGCGAGGGCTTGTGGGTAATCTCGTACCTTTACAAACAAGTGATTCCCCTCTGTGCCCTGATAAATTAACACTTCAGT
AAATTTGCCAGGAAGTTTTCTGGTGTCAAATTTATTAAAACCATATCAACA

Alignment

ORF - retro_ogar_1147 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.79 %
• Parental protein coverage: 63.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DPNADTEWNDILRKKGILPSKESLKDLEKE-AEEEEQRALQQSVVKTYEDMTLEELEDHEDEFNEEDERA
          DPNADT.WN.IL.KKGILP.KE.L..L.KE...E.E.....Q.V....E..T.EELE.HEDEF.EEDE..
Retrocopy DPNADTKWNAILCKKGILPLKETLSELKKE>KSEKEEQRVLQHVEVKHEARTWEELESHEDEFEEEDECT

Parental  IEMYRQQRLAEWKASQLKNKFGEVLEISGKDYVQEVTKAGEGVWVILHLYKQGIPLCALINQYFSELARK
          IEMY.QQ.LAEWKA..L.NK....L.ISGK.YVQEVTKA.EG.WVI..LYKQ.IPLCALIN..FS..ARK
Retrocopy IEMYMQQSLAEWKATELENKC-SILHISGKNYVQEVTKASEGLWVISYLYKQVIPLCALIN*HFSKFARK

Parental  FPDVKFIKAIST
          F..VKFIK.IST
Retrocopy FSGVKFIKTIST

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_1147 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 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002226	1 retrocopy	retro_cfam_1740,
Callithrix jacchus	ENSCJAG00000010160	3 retrocopies	retro_cjac_1486, retro_cjac_1599, retro_cjac_2055,
Dipodomys ordii	ENSDORG00000012397	1 retrocopy	retro_dord_702,
Erinaceus europaeus	ENSEEUG00000000224	1 retrocopy	retro_eeur_506,
Homo sapiens	ENSG00000115539	7 retrocopies	retro_hsap_1132, retro_hsap_151, retro_hsap_2684, retro_hsap_2757, retro_hsap_3535, retro_hsap_3961, retro_hsap_4102,
Myotis lucifugus	ENSMLUG00000016446	1 retrocopy	retro_mluc_1443,
Monodelphis domestica	ENSMODG00000001489	1 retrocopy	retro_mdom_734,
Mus musculus	ENSMUSG00000026078	1 retrocopy	retro_mmus_2284,
Nomascus leucogenys	ENSNLEG00000014393	8 retrocopies	retro_nleu_1499, retro_nleu_1575, retro_nleu_2741, retro_nleu_2891, retro_nleu_538, retro_nleu_571, retro_nleu_778, retro_nleu_926,
Oryctolagus cuniculus	ENSOCUG00000001469	2 retrocopies	retro_ocun_1035, retro_ocun_920,
Otolemur garnettii	ENSOGAG00000015138	2 retrocopies	retro_ogar_1147 , retro_ogar_2959,
Ochotona princeps	ENSOPRG00000011600	2 retrocopies	retro_opri_1070, retro_opri_289,
Tursiops truncatus	ENSTTRG00000006242	1 retrocopy	retro_ttru_1184,