RetrogeneDB ID: retro_ogar_2680

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873646.1:5449416..5450525(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPID
• Ensembl ID: ENSOGAG00000003317
• Aliases: None
• Description: peptidylprolyl isomerase D [Source:HGNC Symbol;Acc:9257]

Sequence

>retro_ogar_2680
ATGTCACACCCGTCCCCCCAGGCTAAGCCCTCCAACCCCAGTAATCCCTGGGTCTTTGATGTGGACATTGGAGGGGAGCG
AGTTGGTCGAATTGTCTTAGAATTGTTTGCAGATATCGTACCTAAAAGTGCAGAAATTTTTTGTGCATTATGTACAGGAG
AAAAAGGTATTGGATCTACGACTGGGAAACCTCTCTATTTCAAAGGATGCCCTTTCCATCACATTATTTTAAAAAAAATT
ATGATTCAGGGTGGAGATTTCTCAAATCAGGATGGAACCGGTGGAGAAAGTATTTATGGTGAAAAATTTGAAGATGAAAA
TTTCTATTATAAGCATGATTGCAAGGGTTTATTGAGCATGGCAAATGCAGGCAGAAATACAAATGGTTCTCAGTTCTTTA
TCACAACAGTTCCAACTCCTCATTCGGATGGAAAACATGTGGTGTTTGGCCAAGTAATTAAAGGAATAGGTGTAGCAAGG
ATACTGGAAAACGTAGAAGTACAAGGTGAAAAACCTTTCAAATTGTGCATTATTGCAGAATGTGGAGAATTGAAGGAAGG
GGATGATAGGGGAATATTCCCCTAAGATGGCTCTGGCAACAGTCATCCAGATTTCCCTGAGGATATGGATATTGATTTAA
AGGATGTAGCTAAAATTTTATTAATAATAGAAGACTTAAAAAACATTGAAAATAATCTTTTCAAAGCCCAGAACTGGGAG
ATGGCCATTAAAAAATATGCAAAAGTTTTAAGGTACGTAGATGTTCAAAGGCTGTTATTGAGAAAGCTGACAGATCTAAA
CTACAACCTATAGCTTTAAGCTGTGTACTGAATATTGGTGCTTGTAAACTGAAGATGTTGAATTGGCAGGGAGTGATTGA
CAGTTGTCTGGAGGCTCTTGAAATAGACTCATCAAATACCAAAGCTCTATACTGCAAAGCTCAAGGATGGCAGGGATTAA
AAGAATATGATCAAGCATTGGCTGATCTTTAAAAAGCTCAGGAGATAGCACCAGAAGATAAAGCTATCCAGGCAGAATTA
CTGAAAGTCAAACAGAAGATAAAGGCACAGAAAGACAAAGAGAAGGCAGTATATGCAAAAGTGTTTGCT

Alignment

ORF - retro_ogar_2680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSHPSPQAKPSNPSNPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGSTTGKPLYFKG
          MSHPSPQAKPSNPSNP.VF.DVDIGGERVGRIVLELFADIVPK.AE.F.ALCTGEKGIGSTTGKPLYFKG
Retrocopy MSHPSPQAKPSNPSNPWVF-DVDIGGERVGRIVLELFADIVPKSAEIFCALCTGEKGIGSTTGKPLYFKG

Parental  CPFHRIIKKF-MIQGGDFSNQDGTGGESIYGEKFEDENFYYKHDREGLLSMANAGRNTNNTNGSQFFITT
          CPFH.II....MIQGGDFSNQDGTGGESIYGEKFEDENFYYKHD..GLLSMANAGR...NTNGSQFFITT
Retrocopy CPFHHIIXXXXMIQGGDFSNQDGTGGESIYGEKFEDENFYYKHDCKGLLSMANAGR---NTNGSQFFITT

Parental  VPTPHLDGKHVVFGQLIKGLGVARILENVEVQGEKPAKLCIIAECGELKEGDDWGIFPKDGSGDSHPDFP
          VPTPH.DGKHVVFGQ.IKG.GVARILENVEVQGEKP.KLCIIAECGELKEGDD.GIFP.DGSG.SHPDFP
Retrocopy VPTPHSDGKHVVFGQVIKGIGVARILENVEVQGEKPFKLCIIAECGELKEGDDRGIFP*DGSGNSHPDFP

Parental  EDADIDLKDVAKILLITEDLKNIGNNLFKAQNWEMAIKKYAKVLRRYVD-GSKAVIEKADRSKLQPIALS
          ED.DIDLKDVAKILLI.EDLKNI.NNLFKAQNWEMAIKKYAKVLR.YVD..SKAVIEKADRSKLQPIALS
Retrocopy EDMDIDLKDVAKILLIIEDLKNIENNLFKAQNWEMAIKKYAKVLR-YVD<CSKAVIEKADRSKLQPIALS

Parental  CVLNIGACKLKMSNWQGAIDSCLEALEIDPSNTKALYRKAQGWQGLKEYDQALLKADLKKAQEIAPEDKA
          CVLNIGACKLKM.NWQG.IDSCLEALEID.SNTKALY.KAQGWQGLKEYDQAL..ADL.KAQEIAPEDKA
Retrocopy CVLNIGACKLKMLNWQGVIDSCLEALEIDSSNTKALYCKAQGWQGLKEYDQAL--ADL*KAQEIAPEDKA

Parental  IQAELLKVKQKIKAQKDKEKAVYAKMFA
          IQAELLKVKQKIKAQKDKEKAVYAK.FA
Retrocopy IQAELLKVKQKIKAQKDKEKAVYAKVFA

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_2680 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 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016680	1 retrocopy	retro_btau_1672,
Choloepus hoffmanni	ENSCHOG00000012069	1 retrocopy	retro_chof_1533,
Callithrix jacchus	ENSCJAG00000001437	2 retrocopies	retro_cjac_2321, retro_cjac_4162,
Echinops telfairi	ENSETEG00000012655	2 retrocopies	retro_etel_10, retro_etel_633,
Felis catus	ENSFCAG00000028926	2 retrocopies	retro_fcat_494, retro_fcat_559,
Myotis lucifugus	ENSMLUG00000009317	1 retrocopy	retro_mluc_1667,
Macaca mulatta	ENSMMUG00000017768	2 retrocopies	retro_mmul_281, retro_mmul_348,
Mustela putorius furo	ENSMPUG00000018108	1 retrocopy	retro_mputfur_1415,
Oryctolagus cuniculus	ENSOCUG00000006602	1 retrocopy	retro_ocun_1625,
Otolemur garnettii	ENSOGAG00000003317	2 retrocopies	retro_ogar_2355, retro_ogar_2680 ,
Pongo abelii	ENSPPYG00000015159	1 retrocopy	retro_pabe_3594,
Rattus norvegicus	ENSRNOG00000027408	1 retrocopy	retro_rnor_188,
Ictidomys tridecemlineatus	ENSSTOG00000001552	1 retrocopy	retro_itri_1422,