RetrogeneDB ID: retro_ggor_676

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 11:112445116..112446049(+)
• Located in intron of: ENSGGOG00000008842

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC1
• Ensembl ID: ENSGGOG00000011741
• Aliases: None
• Description: Histone deacetylase [Source:UniProtKB/TrEMBL;Acc:G3R7V7]

Sequence

>retro_ggor_676
ATGGCGCAAAGGCAGGGCACCAGGAGGAAAGTCTGTTACTACTACGATAGGGGTGTTGGAAATTACTATTATGGACAAGC
CCACCCAAGGAATCCTCACTGAATCTGCATGACTCATAATTTGCTGCTCAACTATGGTTTCTACTGAAAAATGGAAACCC
ATCACCCTCACAAAGCCAATGCTGAGGAGATGACCAAGTACCACAGTGATGACTACATTAAATTCTTGTGCTCCATCTGT
CCAGATTACATGTCTGAGCACAGCAAGTGGATGCAGAGATTCAACGTTAGTGAGGACTGTCCAGCATTTGATGGCCTGTT
TGACTTCTGTCAGTTGTCTACTGGTGGCTCTGTGGCAAGTGCTGTGAAACTTAATGAGCAGCAGATGGACACTGCTGTGA
ATTGGGCTGGAGGCCTGCACCATGCAAAGAAGTTCAAGGCATCTGGCTTCTGTTATGTTAATGATACAATCTGGGCCACC
TTGGAACTGCTAAAGTATCACCAGAGGGTGTTGTATGTTGACGTTGATATTCACCATGATGATGGCATGGAAGAGGCCTT
CTATATTACAGGCTAGGCCAGGACTGTGTCCTTTCATAAATATGGAGAGTACTTCCCAGGAGATGGGGACTTATGGGTTA
CTGGGGCTGGCAAAGGCAGATATTATGCTATTAACTATCTGCTCCTAGATGGGATTGATGATGAGTCCTGTGAGGCCATT
TTCAAACTGGTCATGTCCGAAGTAATAGAGATGTTCCTGTCTAGTGTGGTGATCTTACAGCATGGCTCAGATGCCTTGTC
TAGGGGTCACTTAGATTGCTTTAATCTGATCATCAAAGGGCATGCCAAGTGTGTGGAATCTGTCAAGAGTGTCAACCTGC
CTATGTTATTGATGGCAGAAGGTGGTTACACCATTTATAATGTTGCTCAGTGC

Alignment

ORF - retro_ggor_676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.49 %
• Parental protein coverage: 64.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQTQGTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSD
          MAQ.QGTRRKVCYYYD..VGNYYYGQ.HP..PH.I.MTHNLLLNYG.Y.KME...PHKANAEEMTKYHSD
Retrocopy MAQRQGTRRKVCYYYDRGVGNYYYGQAHPRNPH*ICMTHNLLLNYGFY*KMETHHPHKANAEEMTKYHSD

Parental  DYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLH
          DYIKFL.SI.PD.MSE.SK.MQRFNV.EDCP.FDGLF.FCQLSTGGSVASAVKLN.QQ.D.AVNWAGGLH
Retrocopy DYIKFLCSICPDYMSEHSKWMQRFNVSEDCPAFDGLFDFCQLSTGGSVASAVKLNEQQMDTAVNWAGGLH

Parental  HAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGD
          HAKK..ASGFCYVND...A.LELLKYHQRVLY.D.DIHH.DG.EEAFY.T....TVSFHKYGEYFPG.GD
Retrocopy HAKKFKASGFCYVNDTIWATLELLKYHQRVLYVDVDIHHDDGMEEAFYITG*ARTVSFHKYGEYFPGDGD

Parental  LRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKG
          L...GAGKG.YYA.NY.L.DGIDDES.EAIFK.VMS.V.EMF..S.V.LQ.GSD.LS...L.CFNL.IKG
Retrocopy LWVTGAGKGRYYAINYLLLDGIDDESCEAIFKLVMSEVIEMFLSSVVILQHGSDALSRGHLDCFNLIIKG

Parental  HAKCVEFVKSFNLPMLMLGGGGYTIRNVARC
          HAKCVE.VKS.NLPML....GGYTI.NVA.C
Retrocopy HAKCVESVKSVNLPMLLMAEGGYTIYNVAQC

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	19.76 RPM
SRP007412_cerebellum	0.20 RPM	12.41 RPM
SRP007412_heart	0.00 RPM	20.58 RPM
SRP007412_kidney	0.00 RPM	64.69 RPM
SRP007412_liver	0.00 RPM	68.16 RPM
SRP007412_testis	0.21 RPM	107.43 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_676 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_676 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_826
Macaca mulatta	retro_mmul_1085

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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,