RetrogeneDB ID: retro_nleu_259

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397262.1:48038370..48039702(+)
• Located in intron of: ENSNLEG00000007326

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC1
• Ensembl ID: ENSNLEG00000002473
• Aliases: None
• Description: Histone deacetylase [Source:UniProtKB/TrEMBL;Acc:G1QQE9]

Sequence

>retro_nleu_259
ATGGCGCAAAGGCAGGGCACCAGGAGGAAAGTCTGTTACTACTACGATAGGGATGTTGGAAATTACTATTATGGACAAGC
CCACCCACGGAAGCCTCACTGAATCTGCATGACTCATAATTTGCTGCTCAACTATGGTTTCTAGTGAAAAATGGAAACCC
ATCACCCTCACACAGCCAATGCTGAGGAGTTGACCAAGTACCACAGTAATGACTACATTAAATTATTGTGCTCCATCTGT
TGAGATTACATGTCTGAGCCCAGCAAGCAGATGCAGAGATTCAGTGTTAGTGAGGACTGTCCAGCATTTGATGGCCTGTT
TGACGTCTGTCAGTTGTCTACTGGTGGCTCTGTGGCAAGTGCTGTGAAGCTTAATGAGCAGCAGATGGACATTGCTGTGA
ATTGGGCTGGAGGCCTGCACCATGCAAAGAAGTTCAAGGCATCTGGCTTCTGTTATGTTAATGATACAATCTGGGCCACC
TTGGAACTGCTAAAGTATCACCAGAGGGTGTCGTATGTTGACGTTGATCTTCACCATGATGATGGCATGGAAGAGGTCTT
CTATATTACAGGCTAGGTCAGGACTGTGTCCTTTCATAAATATGGAGAGTACTTCCCAGGAAATGGGGACTTATGGGTTA
TTGGGGCTGGCAAAGGCAAATATTATGCTATTAACTATCTGCTCCTAGATGGGATTGATGATGAGTCCTATGAGGCCATT
TTCAAACTGGCCATGTCCAGAGTAATAGAGATGTTCCTGTCTAGTGTGGTGATCTTACAGCATGGCTCAGATGCCTTGTC
TAGGGGTCACTTAGATTGTTTTATTCTGATCATCAAAGGGCATGCCAAGTGTGTGGAATCTGTCAAGAGCATCAACCTGC
CTATGTTATTGATGGCAGAAGGTGGTTACACCATTTATAATGTTGCTTAGTGCCTGAAAATAAGAAATAGCTGTGGCTCT
GGATATGGAGATCCCTAATGAGCCTTCATACAATGATTACTTTGAATACTTTGGACCATATTTCAAACCCTACATCAGTC
CTTCCAATATGACTAACAAGAACACTAATGAGTACCTGGAGAAGATTAAACAATGGCTGTTTGAGAACCTAGTAATGCAG
CCCCATCCACCTGCAGTCCAAATGCAGGTGATTCCTGAGGATGCTGTCCCTCAAGAGGGTGGTGATGAGATGAAGAAGAC
CCTGACAAGCTCATCTCCATCAGTATCTCTGACAGATGAATTACCTATGAGGAAGAGTTCTTTGGCTCTGATGAGGAGGG
AGAGGGCAGCTGCAAGATCTCTCCCACCTTCAAAAAAGCCAAGAGGGTTAAA

Alignment

ORF - retro_nleu_259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.89 %
• Parental protein coverage: 92.12 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAQTQGTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSD
          MAQ.QGTRRKVCYYYD.DVGNYYYGQ.HP.KPH.I.MTHNLLLNYG...KME...PH.ANAEE.TKYHS.
Retrocopy MAQRQGTRRKVCYYYDRDVGNYYYGQAHPRKPH*ICMTHNLLLNYGF**KMETHHPHTANAEELTKYHSN

Parental  DYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLH
          DYIK.L.SI..D.MSE.SKQMQRF.V.EDCP.FDGLF..CQLSTGGSVASAVKLN.QQ.DIAVNWAGGLH
Retrocopy DYIKLLCSIC*DYMSEPSKQMQRFSVSEDCPAFDGLFDVCQLSTGGSVASAVKLNEQQMDIAVNWAGGLH

Parental  HAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGD
          HAKK..ASGFCYVND...A.LELLKYHQRV.Y.D.D.HH.DG.EE.FY.T..V.TVSFHKYGEYFPG.GD
Retrocopy HAKKFKASGFCYVNDTIWATLELLKYHQRVSYVDVDLHHDDGMEEVFYITG*VRTVSFHKYGEYFPGNGD

Parental  LRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKG
          L..IGAGKGKYYA.NY.L.DGIDDESYEAIFK..MS.V.EMF..S.V.LQ.GSD.LS...L.CF.L.IKG
Retrocopy LWVIGAGKGKYYAINYLLLDGIDDESYEAIFKLAMSRVIEMFLSSVVILQHGSDALSRGHLDCFILIIKG

Parental  HAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTY-ETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSN
          HAKCVE.VKS.NLPML....GGYTI.NVA.C....E.AVALD.EIPNE..YNDYFEYFGP.FK..ISPSN
Retrocopy HAKCVESVKSINLPMLLMAEGGYTIYNVA*CLKI>EIAVALDMEIPNEPSYNDYFEYFGPYFKPYISPSN

Parental  MTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDE-DEEDPDKRISICSSDKRIACEE
          MTN.NTNEYLEKIKQ.LFENL.M.PH.P.VQMQ.IPEDA.P.E.GDE.DEEDPDK.ISI..SD..I..EE
Retrocopy MTNKNTNEYLEKIKQWLFENLVMQPHPPAVQMQVIPEDAVPQEGGDE<DEEDPDKLISISISDR*ITYEE

Parental  EFSDSEEEGEGGRKNSSNFKKAKRVK
          EF..S.EEGEG..K.S..FKKAKRVK
Retrocopy EFFGSDEEGEGSCKISPTFKKAKRVK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_259 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Callithrix jacchus	ENSCJAG00000000970	2 retrocopies	retro_cjac_2490, retro_cjac_830,
Homo sapiens	ENSG00000116478	1 retrocopy	retro_hsap_826,
Gorilla gorilla	ENSGGOG00000011741	1 retrocopy	retro_ggor_676,
Myotis lucifugus	ENSMLUG00000013837	1 retrocopy	retro_mluc_283,
Macaca mulatta	ENSMMUG00000009948	2 retrocopies	retro_mmul_1085, retro_mmul_2518,
Mus musculus	ENSMUSG00000028800	1 retrocopy	retro_mmus_153,
Nomascus leucogenys	ENSNLEG00000002473	1 retrocopy	retro_nleu_259 ,
Pelodiscus sinensis	ENSPSIG00000004134	1 retrocopy	retro_psin_44,
Pteropus vampyrus	ENSPVAG00000013325	1 retrocopy	retro_pvam_1339,
Rattus norvegicus	ENSRNOG00000009568	3 retrocopies	retro_rnor_1091, retro_rnor_1098, retro_rnor_2457,
Sarcophilus harrisii	ENSSHAG00000008787	1 retrocopy	retro_shar_573,