RetrogeneDB ID: retro_cfam_2068

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:41662369..41663319(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RDH12
• Ensembl ID: ENSCAFG00000016446
• Aliases: None
• Description: retinol dehydrogenase 12 (all-trans/9-cis/11-cis) [Source:HGNC Symbol;Acc:19977]

Sequence

>retro_cfam_2068
AAGATGCTGGTTACCTTGGGACAGCTCACCTCCTTCCTTTCTTTCCTATATATAATAGTTATATCCATTAAGCTGTTCTT
TGCTGCTGGGGTTTGGAGAACAAACATGCAGCTTCCCAGGAAGATAGTGGTAATTACCAGAGCCAACATAGGCATCAGCA
AGGAGACGGCCAGAGAGCTTGGTAGCAGAGAAGCCCAAGTATGCATTGCCTACTGAGATATACTGAAGGCATCATCTGCT
GGCCAGTGAATTCCAGGCCAATACAAAGAACTCTCAGATGCTAATTCAGAAACTGGACCCATCTAATACCAAATCCATCT
GAGCTTTTGCTAAAGGCTTTCTGGCAGAGAAAAAGCAGCTCCATATTCTGATCAACAATGCAGGAATGGTGATGTATCCA
TATTCCAAAACAGCTGGTGACTTTGAGACTCACCTGCGAGTCAACCACCTAGTCCACTTTCTTTGTACCCATTTGCTCTT
GGAGCCACCAAAAAAGTCTGTGCCCTCACAGGTGATGAGCCTGTCATCAGTAAGCCACCACACTGGCAAGATTCACTTCC
ACAACCTCCAGGGTGAGAAACACTACAGCTGGGGATTTTGCTCATTGCCACAACCAAGTGGCCAATGTGTTTTTAATTGG
GAATTGGCCAAGAGACTCCAAGACATAGGGGTCACCACTTATGCAGTGCACTCAGGCATCATCTACCCCTGACTAGTCTG
GCACTCCTTCCTGCTGTGTCTGTTCTGGAGGCTCTTCTCCCCTTTATCAAGTCAACATGGTAGGGAGCATAGACCAGGCT
GTACTGTGCCTTAGCTGAGAGCCTGGTGCCCCTGTGTGGCAAGTACTTTGGTGACTGCAAGATGACCTGGGTGCCCCTAG
GGGTCTGAAATAGCAAAACCATTGAGCACCTGTGGAATGTCGCTGTGAGCTTCTAAAAATACACTGGGAG

Alignment

ORF - retro_cfam_2068 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.42 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KMLAILGLLTSFLSFLYVIAPSIRKFFAGGVCRSNVQLPGKVVVITGANTGIGKETARELARRVLAPGAR
          KML..LG.LTSFLSFLY.I..SI..FFA.GV.R.N.QLP.K.VVIT.AN.GI.KET....AR......A.
Retrocopy KMLVTLGQLTSFLSFLYIIVISIKLFFAAGVWRTNMQLPRKIVVITRANIGISKET----ARELGSREAQ

Parental  VYIACRDVLKGESA-ASEIRADTKNSQVLVRKLDLSDTKSIRAFAEGFLAEEKQLHILINNAGVMMCPYS
          V.IA..D.LK..SA.ASE..A.TKNSQ.L..KLD.S.TKSI.AFA.GFLAE.KQLHILINNAG..M.PYS
Retrocopy VCIAY*DILKASSA>ASEFQANTKNSQMLIQKLDPSNTKSI*AFAKGFLAEKKQLHILINNAGMVMYPYS

Parental  KTADGFETHLGVNHLGHFLLTHLLLERLKESTPARVVNLSSVAHHIGKIHFHDLQGEKRYSRG-FAYCHS
          KTA..FETHL.VNHL.HFL.THLLLE..K.S.P..V..LSSV.HH.GKIHFH.LQGEK.YS.G.FA.CH.
Retrocopy KTAGDFETHLRVNHLVHFLCTHLLLEPPKKSVPSQVMSLSSVSHHTGKIHFHNLQGEKHYSWG>FAHCHN

Parental  KLANM-LFTRELAKRLQGTGVTTYAVHPGVVSSELVRHSFLLCLLWRIFS-PFVKSAREGAQTSLHCALA
          ..AN...F..ELAKRLQ..GVTTYAVH.G.....LV.HSFLLCL.WR.FS.PF.KS...GA.T.L.CALA
Retrocopy QVANV<VFNWELAKRLQDIGVTTYAVHSGIIYP*LVWHSFLLCLFWRLFS<PFIKSTW*GA*TRLYCALA

Parental  EGLEPLSGKYFSDCKRAWVSPRARDNKTAERLWNVS-CELLGIQWD
          E.L.PL.GKYF.DCK..WV.......KT.E.LWNV..CELL.I.W.
Retrocopy ESLVPLCGKYFGDCKMTWVPLGV*NSKTIEHLWNVA<CELLKIHWE

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
SRP012049_cerebellum	0.00 RPM	0.08 RPM
SRP017611_brain	0.00 RPM	0.08 RPM
SRP017611_kidney	0.00 RPM	0.20 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2068 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2068 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2068 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_1059

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008036	1 retrocopy	retro_amel_673,
Canis familiaris	ENSCAFG00000016446	1 retrocopy	retro_cfam_2068 ,
Felis catus	ENSFCAG00000014092	1 retrocopy	retro_fcat_1910,
Loxodonta africana	ENSLAFG00000022637	1 retrocopy	retro_lafr_847,
Macropus eugenii	ENSMEUG00000001473	1 retrocopy	retro_meug_41,
Meleagris gallopavo	ENSMGAG00000011960	1 retrocopy	retro_mgal_16,
Microcebus murinus	ENSMICG00000010855	1 retrocopy	retro_mmur_432,
Ornithorhynchus anatinus	ENSOANG00000015759	1 retrocopy	retro_oana_89,
Procavia capensis	ENSPCAG00000009359	1 retrocopy	retro_pcap_1,
Pelodiscus sinensis	ENSPSIG00000010721	1 retrocopy	retro_psin_24,
Sarcophilus harrisii	ENSSHAG00000012445	1 retrocopy	retro_shar_41,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,