RetrogeneDB ID: retro_rnor_1098

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:29556869..29558037(+)
• Located in intron of: None

Retrocopy information

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

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_1098
AAAATCTATCGTCCTCACAAAGCCAGTGCTGAGGAGATGACTAAGTACCACAGCGAGGACTACATTAAATTCTTGCGTTC
TATTCGCCCAGATAATATGTCTGAATACAGCGAGCAGATGCAGAGATTCAACGTGGGTGAGGACTGTCCGGTATTCGATG
GCTTGTTTGAGTTCTGTCAGTAGTCCGCGGGTGGCTGTGTCGAAAGTGCTGTGAAACTCAATAAGCAGCAGACAGACATC
GCTGTGAATTGGGCTGGGGGCCTGCACCATGTAAAAAAAGTCTGAAGCATCTGGCTTCTGTTACGTCAATGATATCGTCT
TGGCCATCCTGGAACTGCTAAAGTATCTCCAGAGGCTGCTGTATATTGACATTGATATTCACCATGGCGATGGCGTAGAA
GAGGCCTTCTATACTACAGACGGGGTCATGACTGTGTCCTTTTATAAATATGGAGAGTACTTCCCAGGAACTGGGGACCT
ACGGGATATTGGAGCTGACACAGGCAAGTACTACGCCATTAACTACCCACTGCGAGACGGCACTGATGATGAGTCCTATG
AAGCCATCTTCAAGCCAGTCATGTCCAAAGTAATGGAGATGTTTCAGCCTAGTGCAGTGGTCCTACAGAGCGGCTCAGAC
TCCCGGTCTGGGGATCGGCTAGGTTGCTTCATTCTGACCCTCAAAGGACACGCCGAGTGTGTGGAGTTCGTGAAGAGTTT
CAACTTGCCGATGCTAATGCTGGGAGGAGGTGGCTACACCATCCGTAATGTCGCTCGGTGCTGGACTTACAAAACAGCTG
TGGCTCTGGACACAGAGATCCCTAATGAGCTACCCTACAATGAGTACTTTGAATACTTTAGACCAGATTTCAGGCTTCAC
ATCAGCCCTTCCAATATGACTAACCAGACCACTTAATGAATACCTAGAAAAGATCAAGCAGTGGCACTTTGAGAACTTGA
GAATGCTGCCCCATGCCCCTGGGATCCAAATGCAGGCCATCCAGAGGATGCCATCCCAGAAGAGAGCGGTGATGATGATG
AGGAAGACCCTGACAAACGAATTTCCATCTGCTCCTCTGACAAACGCATTGCCTGTGAGGAGGAATTCCCTGATTCTGAT
GAGGAGGGAGAAGGAGGTCTCGAGAACTCTTCCAACTTCAAAAAAGCC

Alignment

ORF - retro_rnor_1098 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.56 %
• Parental protein coverage: 80.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EIYRPHKANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASA
          .IYRPHKA.AEEMTKYHS.DYIKFLRSIRPDNMSEYS.QMQRFNVGEDCPVFDGLFEFCQ.S.GG.V.SA
Retrocopy KIYRPHKASAEEMTKYHSEDYIKFLRSIRPDNMSEYSEQMQRFNVGEDCPVFDGLFEFCQ*SAGGCVESA

Parental  VKLNKQQTDIAVNWAGGLHHAKK-SEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTT
          VKLNKQQTDIAVNWAGGLHH.KK.SEASGFCYVNDIVLAILELLKY.QR.LYIDIDIHHGDGVEEAFYTT
Retrocopy VKLNKQQTDIAVNWAGGLHHVKK>SEASGFCYVNDIVLAILELLKYLQRLLYIDIDIHHGDGVEEAFYTT

Parental  DRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQ
          D.VMTVSF.KYGEYFPGTGDLRDIGA..GKYYA.NYPLRDG.DDESYEAIFKPVMSKVMEMFQPSAVVLQ
Retrocopy DGVMTVSFYKYGEYFPGTGDLRDIGADTGKYYAINYPLRDGTDDESYEAIFKPVMSKVMEMFQPSAVVLQ

Parental  CGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPY
          .GSDS.SGDRLGCF.LT.KGHA.CVEFVKSFNLPMLMLGGGGYTIRNVARCWTY.TAVALDTEIPNELPY
Retrocopy SGSDSRSGDRLGCFILTLKGHAECVEFVKSFNLPMLMLGGGGYTIRNVARCWTYKTAVALDTEIPNELPY

Parental  NDYFEYFGPDFKLHISPSNMTNQNT-NEYLEKIKQRLFENLRMLPHAPGVQMQAI-PEDAIPEESGDEDE
          N.YFEYF.PDF.LHISPSNMTNQ.T.NEYLEKIKQ..FENLRMLPHAPG.QMQAI.PEDAIPEESGD.DE
Retrocopy NEYFEYFRPDFRLHISPSNMTNQTT>NEYLEKIKQWHFENLRMLPHAPGIQMQAI<PEDAIPEESGDDDE

Parental  EDPDKRISICSSDKRIACEEEFSDSDEEGEGGRKNSSNFKKA
          EDPDKRISICSSDKRIACEEEF.DSDEEGEGG..NSSNFKKA
Retrocopy EDPDKRISICSSDKRIACEEEFPDSDEEGEGGLENSSNFKKA

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_1098 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1098 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1098 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,