RetrogeneDB ID: retro_ogar_314

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873520.1:8295314..8297334(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000003061
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HSPA4L
• Ensembl ID: ENSOGAG00000005754
• Aliases: None
• Description: heat shock 70kDa protein 4-like [Source:HGNC Symbol;Acc:17041]

Sequence

>retro_ogar_314
AGCCCGTTGTTGACTGTTGTTTCGGTTCCTCGTTTCTATACCGATGCAGAAAGACGATCGGTGATGGATGCTACACAGAT
TGCAGGTCTCAATTGCCTGCGATTAATGAATGAAACTACTGCAGTTGCTCTTGCATGTGGAATCTATAAGCAAGATCTTC
CTGCCTTAGAAGAGAAACCAAGAAATGTAGTTTTTGTAGACATGGGCCATTCTGCTTATCAAGTTTCTGTATGTGCATTT
AATAGAGGAAAACTGAAGGTTCTGGCCACTGCATTTGACACAACACTGGGAGGCAGAAAATTTGATGAAGTTTTAGTAAA
TCACTTCTGTGAAGAATTTGGGAAGAAATACAAGCTAGACATAAAGTCCAAAATCCGTGCATTATTACGACTCTCTCAGG
AGTGTGAGAAACTCAAGAAATTGATGAGTGCAAATGCTTCAGATCTCCCTCTGAGCATTGAGTGTTTTATGAATGACATT
GATGTATCTGGAACTATGAATAGAGGCAAATTTCTGGAAATGTGCGATGATCTCTTAGCTAGAGTGGAGCCACCACTTCG
TAGTGTTTTGGAACAAGCCAGGTTAAAGAAAGAAGATATTTATGCAGTGGAGATAGTTGGTGGTGCTACAAGAATTCCTG
CAGTAAAAGAGAAGATCAGCAAATTTTTTGGTAAAGAACTTAATACAACATTAAATGCTGATGAAGCTGTCACTCGAGGC
TGTGCATTGCAGTGTGCAATCTTATCACCTGCTTTCAAAGTCAGAGAATTTTCTGTCACTGATGTACTACCCTATCCAAT
CTCTCTGAGATGGAATTCTACAGCTGAAGAAGGGTCAAGTGACTGTGAAGTCTGCAAAAAATCATGCTGCTCCTTTCTCT
AAAGTTCTCACATTTTATAGAAAGGAACCTTTCACTCTTGAGGCCTATTACAGCTTTCCTCGGGAGTTGCCCTACCCAGA
TCCTGCTATAGCCCAGTTTTCAGTTCAGAAAGTCACTCCTCAGTCTGATGGCTCCAGTTCAAAAGTGAAAGTCAAGGTTC
GAGTAAATGTCCATGGCATTTTCAGTGTGTCTAGTGCATCCCTAGCAGAAGTACATAAGTCTGAGGAAAATGAGGAACCA
ATGGAAACAGACCAGAATGCGAAGGAGGAAGAGAAGATGCAGGTGGACCAGGAGGAAGCTCATGTGGAAGAGCAACAGCA
GCAGACGCCAGCAGAAAACAAGGCAGAGTCTGAAGAAATGGAGACTTCCCAAGCTGGATCAAAAGATAAAAAGATGGACC
AACCACCCCAAGCCAAGAAGGCAAAAGTGAAGACCAGTACTGTGGACCTGCCAATTGAAAATCAGCTATTATGGCAGATA
GACAAAGAGATGCTCAACTTGTACATTGAAAATGAGGGTAAGATGATCATGCAGGATAAACTGGAGAAGGAGCGGAATGA
TGCTAAGAATGCAGTGGAAGAATATGTGTATGAAATGAGAGACAAGCTTAGTGGTGAATATGAGAAGTTTGTGAGCGAAG
ATGATCGTAACAGTTTTACTTTGAAACTAGAAGATACTGAAAATTGGTTATATGAGGATGGAGAAGACCAGCCAAAGCAA
GTTTATGTTGATAAATTGGCTGAATTAAAAAATCTAGGTCAGCCTATTAAGTTACGGTTCCAGGAATCTGGAGAAAGACC
AAGATTATTTGATGAACTAGGGAAACAGATCCAACAATATATGAAAGCAATCAGTTCTTTCAAAAACAAGGAGGACCAGT
ATGACCATTTGGATGCTGCTGACATGATGAAGGTAGAAAAAAGCACAAATGAAGCAATGGAGTGGATGAATGACAAGCTG
AATCTGCAGAACAAACAGAGTCTGACTATGGATCCAGTTGTCAAGTCAAAAGAGATTGAAGCTAAAATTAAGGAGCTGAT
GAGTATCTGTAGCCCCATAATTTCAAAGCCCAAATCCAAAGTGGAACCTCCAAAGGAGGAGCAAAAAAATGCTGAGCAGA
ATGGACCAGTGGATGGACAA

Alignment

ORF - retro_ogar_314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.09 %
• Parental protein coverage: 77.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPEICVLRIPSFFTDAERRSVMAAAQVAGLNCLRLMNETTAVALAYGIYKQDLPPLDEKPRNVIFIDMGH
          SP...V...P.F.TDAERRSVM.A.Q.AGLNCLRLMNETTAVALA.GIYKQDLP.L.EKPRNV.F.DMGH
Retrocopy SPLLTVVSVPRFYTDAERRSVMDATQIAGLNCLRLMNETTAVALACGIYKQDLPALEEKPRNVVFVDMGH

Parental  SAYQVSVCAFNKGKLKVLAAAFDPYLGGRNFDEALVDYFCDEFKTKYKINVKENSRALLRLYQECEKLKK
          SAYQVSVCAFN.GKLKVLA.AFD..LGGR.FDE.LV..FC.EF..KYK...K...RALLRL.QECEKLKK
Retrocopy SAYQVSVCAFNRGKLKVLATAFDTTLGGRKFDEVLVNHFCEEFGKKYKLDIKSKIRALLRLSQECEKLKK

Parental  LMSANASDLPLNIECFMNDLDVSSKMNRAQFEQLCASLLARVEPPLKAVMEQANLQREDISNIEIVGGAT
          LMSANASDLPL.IECFMND.DVS..MNR..F...C..LLARVEPPL..V.EQA.L..EDI...EIVGGAT
Retrocopy LMSANASDLPLSIECFMNDIDVSGTMNRGKFLEMCDDLLARVEPPLRSVLEQARLKKEDIYAVEIVGGAT

Parental  RIPAVKEQITKFFLKDISTTLNADEAVARGCALQCAILSPAFKVREFSITDIVPYSITLRWKTSFEDGTG
          RIPAVKE.I.KFF.K...TTLNADEAV.RGCALQCAILSPAFKVREFS.TD..PY.I.LRW....E.G..
Retrocopy RIPAVKEKISKFFGKELNTTLNADEAVTRGCALQCAILSPAFKVREFSVTDVLPYPISLRWNSTAEEGSS

Parental  ECEVFC-KNHPAPFSKVITFHKKEPFELEAFYTNLHEVPYPDPRIGSFTIQNVFPQSDGDSSKVKVKVRV
          .CEV.C.KNH.APFSKV.TF..KEPF.LEA.Y....E.PYPDP.I..F..Q.V.PQSDG.SSKVKVKVRV
Retrocopy DCEV-C>KNHAAPFSKVLTFYRKEPFTLEAYYSFPRELPYPDPAIAQFSVQKVTPQSDGSSSKVKVKVRV

Parental  NIHGIFSVASASVIEKQNLEGDHSDIPMETETSIKSENKDDVDKMQVDQEEGAHQKCHAEHTPEEEIDHT
          N.HGIFSV.SAS..E...........PMET....K.E.K..VD......EE...Q.........EE....
Retrocopy NVHGIFSVSSASLAEVH--KSEENEEPMETDQNAKEEEKMQVDQEEAHVEEQQQQTPAENKAESEEMETS

Parental  GAKAKSTPSDKQERLNQTIKKGKVKSIDLPIQSTLCRQLGQDVLNSYIENEGKMIMQDKLEKERNDAKNA
          .A..K....D..........K.K....DLPI...L..Q.....LN.YIENEGKMIMQDKLEKERNDAKNA
Retrocopy QAGSKDKKMDQPPQAKKA--KVKTSTVDLPIENQLLWQIDKEMLNLYIENEGKMIMQDKLEKERNDAKNA

Parental  VEEYVYDFRDKLGTVYEKFITPEDLNKLSAILEDTENWLYEEGEDQPKQVYVDKLQELKKYGQPIQMKYM
          VEEYVY..RDKL...YEKF....D.N.....LEDTENWLYE.GEDQPKQVYVDKL.ELK..GQPI.....
Retrocopy VEEYVYEMRDKLSGEYEKFVSEDDRNSFTLKLEDTENWLYEDGEDQPKQVYVDKLAELKNLGQPIKLRFQ

Parental  EHEERPKALNDLGKKIQLVMKVIEAYRNKDERYDHLDPAEVEKVEKYISDAMSWLNSKMNAQNKLSLTQD
          E..ERP.....LGK.IQ..MK.I....NK...YDHLD.A...KVEK....AM.W.N.K.N.QNK.SLT.D
Retrocopy ESGERPRLFDELGKQIQQYMKAISSFKNKEDQYDHLDAADMMKVEKSTNEAMEWMNDKLNLQNKQSLTMD

Parental  PVVKVSEIVAKSKELDNFCNPIIYKPKPKVEVAEDKAKANSEHNGPMDRQ
          PVVK..EI.AK.KEL...C.PII.KPK.KVE......K.N.E.NGP.D.Q
Retrocopy PVVKSKEIEAKIKELMSICSPIISKPKSKVEPPKEEQK-NAEQNGPVDGQ

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_314 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000005754	1 retrocopy	retro_ogar_314 ,