RetrogeneDB ID: retro_ogar_1760

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873564.1:10765191..10766378(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000028368
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAJA4
• Ensembl ID: ENSOGAG00000006752
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 4 [Source:HGNC Symbol;Acc:14885]

Sequence

>retro_ogar_1760
AAAATGGTGAAAGAAACCACTTACTATGATGTTTTGGAAGTCAAACCCAATGCCACGCACAAAGAATTGAAGAAAGCATA
TAGAAAACTGGCCTTGAAGTACCACCCTGATAAGGATCCAAATGAAGGCGAGAAGTTTAAACAGATTTCTCAAGCTTATG
AAGTTCTCTCTGATGCAAAGAAAACAGAATTATATGACAAAGGAGGAGAACAGGCAATTAGAGAGGGTGGAGCAGGTGGT
GGTTTTGCTTCCCCCATGAACATCTTTGATATGTTTTTTGGAGGAGGAGGAGGAAGGATGCAGAGAAAAAGGAGAGGTAA
AAATGTCATACATCAGCTCTCGGTTACCTTAGAAGATTTATGTAATGGTGCCACAAGAAAACTAGCTCTGCAAAAGAATG
TGATTTGCAACAAATGTGAAGGTCAAGGTGGCAAAAGGGAGCAATAGAGTGCTGTGCCAATTGCCGAGGTACTGGAATGC
AAATAAGAATCCATCAGATAGCACCTGGAATGGTTCAGCAAATTCAATCTGTGTGCATGGGCCATGGAGAACGGATCAGT
CCTAAAGATAGATGTAAAAGCTGCAATGGAAGGAAGATAGTTTGAGAGAAGAAGATTCTGGAAGTTCATATTAACAAAGG
CATGAAAGATGGCCAGAAGATAACATTCCATGGTGAAGGAGACCAAGAACCAGGATTGGAGCCAGGACATATTATCATTG
TGTTAGATCAGAAGGACCATGCTGTCTTTACTCCACGAGAAGAAGACCTTTGCATGTGTATGGACATACAGCTGGTTGAA
ACATTGTGTGGCTTCCAAAAGCCAATAGCTACTCTTGACAACAGAACCATAGTCATCACCTCTCATCCAGGTCAGATCGT
CAAGCATGGAGACATCAAGCGTGTGCCAAATGAAGGCATGCCAATTTATCATAGACCATATGAAAAGGGTCACCTAATCA
TTGAAGTTAAGGTAAACTTTCCTGAAAATGGCTTTCTTTTTCCTGATAAACTCTCATTGCTGGAAAAGCTTCTACCAGAG
AGGAAGGAAGCAGAAGAGACTGATGAAATGGATCAAGTAGAACTGGTGGACTTTGATCCAAATCAGGAAAGATGGCGCCA
TTACAATGGAGAAGCATATGAGGATGATGAACAGCATCCCAGAGGTGGTGTGCAGTGTCAAACCTCT

Alignment

ORF - retro_ogar_1760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.83 %
• Parental protein coverage: 93.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KMVKETQYYDILGVKPSASPEEIKKAYRKLALKYHPDKNPDEGEKFKLISQAYEVLSDPKKRDIYDQGGE
          KMVKET.YYD.L.VKP.A...E.KKAYRKLALKYHPDK.P.EGEKFK.ISQAYEVLSD.KK...YD.GGE
Retrocopy KMVKETTYYDVLEVKPNATHKELKKAYRKLALKYHPDKDPNEGEKFKQISQAYEVLSDAKKTELYDKGGE

Parental  QAIKEGGAGGPSFSSPMDIFDMFFGGGG-RMARERRGKNVVHQLSVTLEDLYNGVTKKLALQKNVICEKC
          QAI.EGGAGG..F.SPM.IFDMFFGGGG.RM.R.RRGKNV.HQLSVTLEDL.NG.T.KLALQKNVIC.KC
Retrocopy QAIREGGAGG-GFASPMNIFDMFFGGGGGRMQRKRRGKNVIHQLSVTLEDLCNGATRKLALQKNVICNKC

Parental  EGIGGK-KGSVEKCPICKGRGMQIHIQQIGPGMVQQIQTVCVECKGQGERINPKDRCESCSGAKVIREKK
          EG.GGK.KG..E.C..C.G.GMQI.I.QI.PGMVQQIQ.V...C.G.GERI.PKDRC.SC.G.K...EKK
Retrocopy EGQGGK<KGAIECCANCRGTGMQIRIHQIAPGMVQQIQSV---CMGHGERISPKDRCKSCNGRKIV*EKK

Parental  IIEVHVEKGMKDGQKILFHGEGDQEPELEPGDVIIVLDQKDHSVFQRRGHDLIMKMKIQLSEALCGFKKT
          I.EVH..KGMKDGQKI.FHGEGDQEP.LEPG..IIVLDQKDH.VF..R..DL.M.M.IQL.E.LCGF.K.
Retrocopy ILEVHINKGMKDGQKITFHGEGDQEPGLEPGHIIIVLDQKDHAVFTPREEDLCMCMDIQLVETLCGFQKP

Parental  IKTLDDRILVITSKSGEVIKHGELKCVRNEGMPIYKAPLEKGTLIIQFLVIFPEKHWLSPEKLPQLEALL
          I.TLD.R..VITS..G...KHG..K.V.NEGMPIY..P.EKG.LII...V.FPE...L.P.KL..LE.LL
Retrocopy IATLDNRTIVITSHPGQIVKHGDIKRVPNEGMPIYHRPYEKGHLIIEVKVNFPENGFLFPDKLSLLEKLL

Parental  PPRQKVRITDDMDQVELKEFNPSEQNWRQH-GEAYEEDDDGPRTGVQCQTA
          P.R.....TD.MDQVEL..F.P....WR...GEAYE.D...PR.GVQCQT.
Retrocopy PERKEAEETDEMDQVELVDFDPNQERWRHYNGEAYEDDEQHPRGGVQCQTS

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_1760 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 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012576	1 retrocopy	retro_amel_1659,
Dipodomys ordii	ENSDORG00000005972	4 retrocopies	retro_dord_245, retro_dord_280, retro_dord_333, retro_dord_533,
Echinops telfairi	ENSETEG00000004320	4 retrocopies	retro_etel_1010, retro_etel_1031, retro_etel_1067, retro_etel_608,
Macropus eugenii	ENSMEUG00000015982	4 retrocopies	retro_meug_1059, retro_meug_1893, retro_meug_292, retro_meug_624,
Microcebus murinus	ENSMICG00000008789	6 retrocopies	retro_mmur_1242, retro_mmur_1460, retro_mmur_39, retro_mmur_482, retro_mmur_496, retro_mmur_578,
Mus musculus	ENSMUSG00000032285	1 retrocopy	retro_mmus_2632,
Otolemur garnettii	ENSOGAG00000006752	5 retrocopies	retro_ogar_1760 , retro_ogar_1985, retro_ogar_221, retro_ogar_2656, retro_ogar_841,
Ochotona princeps	ENSOPRG00000007594	1 retrocopy	retro_opri_1028,
Tupaia belangeri	ENSTBEG00000009268	9 retrocopies	retro_tbel_2276, retro_tbel_2308, retro_tbel_2790, retro_tbel_2831, retro_tbel_3242, retro_tbel_4322, retro_tbel_4735, retro_tbel_772, retro_tbel_796,
Tarsius syrichta	ENSTSYG00000008600	1 retrocopy	retro_tsyr_1752,