RetrogeneDB ID: retro_rnor_1091

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:19441127..19442566(+)
• Located in intron of: ENSRNOG00000008570

Retrocopy information

• Ensembl ID: ENSRNOG00000050958
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hdac1
• Ensembl ID: ENSRNOG00000009568
• Aliases: None
• Description: Histone deacetylase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q4QQW4]

Sequence

>retro_rnor_1091
ATGGTGCAGCCTCAGGGTGTCAAGAGGAAATTCTGTTACTGCTAGGACTGGGATGTCGGAAACTACTATTATGGACAAGG
GCACCCAATGAAGCCTTACTGAATCCGCATGACTCAAAATTTGCTGTCCAACCATGGTCTTTATTGAAAATGGAAATCTA
CCATCCTCACAAAGCCACTGCTGAGGAGATGACCAAGTACCACAGTGATGACTACATTAAATTCTTGCACTCTATTCGCC
CAGATAATATGTCTGAATATAGCAAGCAGATGCAGAGATTCAACAGGGGTGAGGTCTGTCCGGTATTTGATGGCTTGTTT
GAGTTTTGTCGGTTGTCCACGGGTGGCTCTGTGCAAGTGCTGTGAAACTCAATAAGCAGCAGACAGACATCGCTGTGAAC
TGCACTGGGTCCTGCACCACGCAAAGAAGTCTGAAGCATCTGGCTTCTGTTACGTCAATGATATCGTCTTGGCCATCCTG
GAACTGCTGAGGTATCACCAGAGGGTGCTGAATATTGACATTTATATTCCCCGTGGCTATGGTGTGGAAGAGGCCTTCTA
TACAACAGACTGGGTCATGACTGTGTCCTTTTATAAATATGGAGAGTACTTCCCAGGAACTGGGGACCTACGGGATATTG
AGGCTGGCAAAGACAAGTACTATGCCGTTAACTACCCACTGCGAGACGGCATTAATGATGAGTCCTATGAAGCCATCTTC
AAGCCACTCATGTCCAAAGTAATGGAGATGTTCCAGTCTAGTGCAGTGATCTTAGAGTGGGGCTCAGATTCCCTTCTGAG
GATCGGTTAGATTGCTTCAATCTGACTCTCAAAGGGCATGCCAAGTGTGTGGAGTTCGTGAAGAGTTTCAACTTGCCGAT
GCTAATGTTGGGAGGAGGTGGCTACACCCTCCGTAATGTCACTCGGTGCTGGAGTTAAGAAACAGCTGTGGCCAGGGCAC
AGAGATCCCTAAAGAGCTACCCTACAATGACTACTTTGAATACTTTGGACCAGATTTCAAGCTTCACATCAGCCCTTCCA
ATATGACTAACCAGACCACTTAATGAATACCTAGAAAAGATCAAGCAGTGGCACTTTGAGAACTTGAGAATGCTGCCCCA
TGCTCCTAGGGTCCAAATGCAGGCCATACCAGAGGGTGCCATCCCAGAAGAGAGCAGTGAGGAAGATAAGGAAGACCCTG
ACAAACACATCTCCATCTGCTCCTCTGACAAACGCACTGCCTGTGAGGAAGAATTCTCTGATTCAGATGAGGAGGGAGAA
GGTTGTCCCAAGAACTCTTCTAACTTCAAAAAAGCCAAAAGAGTCAAAACAGAGGATGAGAAAAAAAAAGATTCTGAAGA
AAAAGAAGCCACAGAAGAGGAGAAAACCAAGGATGAGAAACCAGAAGCCAAAGGGGTCAAAAAAGAAGTCAATTTGGCC

Alignment

ORF - retro_rnor_1091 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.97 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAQTQGTKRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLY-RKMEIYRPHKANAEEMTKYHS
          M.Q.QG.KRK.CY..D.DVGNYYYGQGHPMKP..IRMT.NLL.N.GLY..KMEIY.PHKA.AEEMTKYHS
Retrocopy MVQPQGVKRKFCYC*DWDVGNYYYGQGHPMKPY*IRMTQNLLSNHGLY<LKMEIYHPHKATAEEMTKYHS

Parental  DDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSV-ASAVKLNKQQTDIAVNWAGG
          DDYIKFL.SIRPDNMSEYSKQMQRFN.GE.CPVFDGLFEFC.LSTGGSV.ASAVKLNKQQTDIAVN..G.
Retrocopy DDYIKFLHSIRPDNMSEYSKQMQRFNRGEVCPVFDGLFEFCRLSTGGSV<ASAVKLNKQQTDIAVNCTGS

Parental  -LHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPG
          .LHHAKKSEASGFCYVNDIVLAILELL.YHQRVL.IDI.I..G.GVEEAFYTTD.VMTVSF.KYGEYFPG
Retrocopy <LHHAKKSEASGFCYVNDIVLAILELLRYHQRVLNIDIYIPRGYGVEEAFYTTDWVMTVSFYKYGEYFPG

Parental  TGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSL-SGDRLGCFNL
          TGDLRDI.AGK.KYYAVNYPLRDGI.DESYEAIFKP.MSKVMEMFQ.SAV.L..GSDSL.S.DRL.CFNL
Retrocopy TGDLRDIEAGKDKYYAVNYPLRDGINDESYEAIFKPLMSKVMEMFQSSAVILEWGSDSL<SEDRLDCFNL

Parental  TIKGHAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVA-LDTEIPNELPYNDYFEYFGPDFKLHI
          T.KGHAKCVEFVKSFNLPMLMLGGGGYT.RNV.RCW..ETAVA...TEIP.ELPYNDYFEYFGPDFKLHI
Retrocopy TLKGHAKCVEFVKSFNLPMLMLGGGGYTLRNVTRCWS*ETAVA<QGTEIPKELPYNDYFEYFGPDFKLHI

Parental  SPSNMTNQNT-NEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKRISICSSDKRI
          SPSNMTNQ.T.NEYLEKIKQ..FENLRMLPHAP.VQMQAIPE.AIPEES..ED.EDPDK.ISICSSDKR.
Retrocopy SPSNMTNQTT>NEYLEKIKQWHFENLRMLPHAPRVQMQAIPEGAIPEESSEEDKEDPDKHISICSSDKRT

Parental  ACEEEFSDSDEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVKMA
          ACEEEFSDSDEEGEG..KNSSN...............D.EE.KE.TEEEKTK.EKPEAKGVK.EV..A
Retrocopy ACEEEFSDSDEEGEGCPKNSSNXXXXXXXXXXXXXXXDSEE-KEATEEEKTKDEKPEAKGVKKEVNLA

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
SRP017611_brain	0.00 RPM	16.90 RPM
SRP017611_kidney	0.00 RPM	40.26 RPM
SRP017611_liver	0.00 RPM	19.90 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1091 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1091 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1091 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 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,
Otolemur garnettii	ENSOGAG00000005709	3 retrocopies	retro_ogar_2181, retro_ogar_3022, retro_ogar_3313,
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,