RetrogeneDB ID: retro_ptro_69

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:80218912..80220307(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039785
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HDAC2
• Ensembl ID: ENSPTRG00000018519
• Aliases: None
• Description: Histone deacetylase [Source:UniProtKB/TrEMBL;Acc:K7B9A4]

Sequence

>retro_ptro_69
GATGTTGGAAATTACTATTATGGACAAGGCCACCCAATGAAGCCTCACCGAATCCGCATGACTCATAATTTGCTGCTCAA
CTATGGTCTCTACCGAAAAATGGAAATCTATCGCCCTCACAAAGCCAATGCTGAGGAGATGACCAAGTACCACAGCGATG
ACTACATTAAATTCTTGCGCTCCATCCGTCCAGATAACATGTCGGAGTACAGCAAGCAGATGCAGAGATTCAACGTTGGT
GAGGACTGTCCAGTATTCGATGGCCTGTTTGAGTTCTGTCAGTTGTCTACTGGTGGTTCTGTGGCAAGTGCTGTGAAACT
TAATAAGCAGCAGACGGACATCGCTGTGAATTGGGCTGGGGGCCTGCACCATGCAAAGAAGTCCGAGGCATCTGGCTTCT
GTTACGTCAATGATATCGTCTTGGCCATCCTGGAACTGCTAAAGTATCACCAGAGGGTGCTGTATATTGACATTGATATT
CACCATGGTGACGGCGTGGAAGAGGCCTTCTATACCACGGACCGGGTCATGACTGTGTCCTTTCATAAGTATGGAGAGTA
CTTCCCAGGAACTGGGGACCTACGGGATATCGGGGCTGGCAAAGGCAAGTATTATGCTGTTAACTACCCGCTCCGAGACG
GGATTGATGACGAGTCCTATGAGGCCATTTTCAAGCCGGTCATGTCCAAAGTAATGGAGATGTTCCAGCCTAGTGCGGTG
GTCTTACAGTGTGGCTCAGACTCCCTATCTGGGGATCGGTTAGGTTGCTTCAATCTAACTATCAAAGGACACGCCAAGTG
TGTGGAATTTGTCAAGAGCTTTAACCTGCCTATGCTGATGCTGGGAGGCGGTGGTTACACCATTCGTAACGTTGCCCGGT
GCTGGACATACGAGACAGCTGTGGCCCTGGATACGGAGATCCCTAATGAGCTTCCATACAACGACTACTTTGAATACTTT
GGACCAGATTTCAAGCTCCACATCAGTCCTTCCAATATGACTAACCAGAACACGAATGAGTACCTGGAGAAGATCAAACA
GCGACTGTTTGAGAACCTTAGAATGCTGCCGCACGCACCCGGGGTCCAAATGCAGGCGATTCCTGAGGACGCCATCCCTG
AGGAGAGTGGCGATGAGGACGAAGAAGACCCTGACAAGCGCATCTCGATCTGCTCCTCTGACAAACGAATTGCCTGTGAG
GAAGAGTTCTCCGATTCTGAAGAGGAGGGAGAGGGGGGCCGCAAGAACTCTTCCAACTTCAAAAAAGCCAAGAGAGTCAA
AACAGAGGATGAAAAAGAGAAAGACCCAGAGGAGAAGAAAGAAGTTACCGAAGAGGAGAAAACCAAGGAGGAGAAGCCAG
AAGCCAAAGGGGTCAAGGAGGAGGTCAAGTTGGCC

Alignment

ORF - retro_ptro_69 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.88 %
• Parental protein coverage: 80.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEY
          D.GNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKA.AEEMTKYHSD.YIKFLRSIRPDNMSEY
Retrocopy DVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSDDYIKFLRSIRPDNMSEY

Parental  SKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIV
          SKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVA.AVKLN.QQTD.AVNWAGGLHHAKKSEASGFCYVNDIV
Retrocopy SKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIV

Parental  LAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFP
          LAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVN.P
Retrocopy LAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYP

Parental  MRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLM
          .RDGIDDESY..IFKP..SKVMEM.QPSAVVLQCG.DSLSGDRLGCFNLT.KGHAKCVE.VK.FNLP.LM
Retrocopy LRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLM

Parental  LGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLF
          LGGGGYTIRNVARCWTYETAVALD.EIPNELPYNDYFEYFGPDFKLHISPSNMTNQNT.EY.EKIKQRLF
Retrocopy LGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLEKIKQRLF

Parental  ENLRMLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEEFSDSEDEGEGGRRNVADH
          ENLRMLPHAPGVQMQAIPEDA..E.SGDED.EDPDKRISI..SDKRIAC.EEFSDSE.EGEGGR.N....
Retrocopy ENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKRISICSSDKRIACEEEFSDSEEEGEGGRKNSSNF

Parental  KKGAKKARIEEDKKETEDKKTDVKEEDKSKDNSGEKTDTKGTKSE
          KK.AK....E..K......K..V.EE.K.K....EK...KG.K.E
Retrocopy KK-AKRVKTEDEKEKDPEEKKEVTEEEKTKE---EKPEAKGVKEE

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	4.61 RPM	25.95 RPM
SRP007412_cerebellum	2.76 RPM	47.10 RPM
SRP007412_heart	7.43 RPM	33.40 RPM
SRP007412_kidney	19.93 RPM	36.69 RPM
SRP007412_liver	13.75 RPM	18.13 RPM
SRP007412_testis	32.56 RPM	78.30 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_69 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_69 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_69 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Echinops telfairi	ENSETEG00000008468	1 retrocopy	retro_etel_488,
Myotis lucifugus	ENSMLUG00000003117	4 retrocopies	retro_mluc_1570, retro_mluc_225, retro_mluc_2548, retro_mluc_935,
Monodelphis domestica	ENSMODG00000017860	1 retrocopy	retro_mdom_597,
Ornithorhynchus anatinus	ENSOANG00000003631	1 retrocopy	retro_oana_79,
Pan troglodytes	ENSPTRG00000018519	1 retrocopy	retro_ptro_69 ,
Sorex araneus	ENSSARG00000000354	1 retrocopy	retro_sara_651,
Ictidomys tridecemlineatus	ENSSTOG00000012779	1 retrocopy	retro_itri_374,
Tarsius syrichta	ENSTSYG00000009363	4 retrocopies	retro_tsyr_1337, retro_tsyr_1355, retro_tsyr_681, retro_tsyr_765,
Tursiops truncatus	ENSTTRG00000015043	1 retrocopy	retro_ttru_462,