RetrogeneDB ID: retro_cfam_2154

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:44096696..44097128(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCTN6
• Ensembl ID: ENSCAFG00000006518
• Aliases: None
• Description: dynactin 6 [Source:HGNC Symbol;Acc:16964]

Sequence

>retro_cfam_2154
CAGAGAAGGCTCAAAAGAGTAAAGATTCCTCCTGGAGCAGTTGTGTATGTAGAAAGTGAAACCTGGGGTGATATAACTAC
AGGACCTAGGACAGTGATTCACTCTAAAGCACAAATTATTGCAGAAGTCAGGCTAATAGTGGGTGAAGTAACCTATTTGA
AGAACAGGTGCTTATCATAAATGCTTACCTTGATAATATCACCCCTAATGCTGATGATCCAGACCTGAAACCTATGATCA
TTGGCACCAATAATGATTTTGAAGTTGGCTGTTATTCCCAAGCCATGAAAAATGGGAAATCATAATGTTATTGTATCAAA
AGCATATGTGGAATGAAATGTAATACTGACAAGTGGTTGCATCACTGTGGCTTGTTGCAATCTGAATACATTTGAGGTCA
TCCCTGAGAATACAGTGATTGATGGTGCAGAC

Alignment

ORF - retro_cfam_2154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.79 %
• Parental protein coverage: 76.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKAQKSVKIAPGAVVCVESEIRGDVTIGPRTVIHPKARIIAEAGPIVIGE-GNLIEEQALIINAHPDNIT
          ....K.VKI.PGAVV.VESE..GD.T.GPRTVIH.KA.IIAE......GE..NL.EEQ.LIINA..DNIT
Retrocopy QRRLKRVKIPPGAVVYVESETWGDITTGPRTVIHSKAQIIAEVR-LIVGE<SNLFEEQVLIINAYLDNIT

Parental  PDAEDPEPKPMIIGTNNVFEVGCYSQAMK-MGDNNVIESKAYVGRNVILTSGCIIGACCSLNTFEVIPEN
          P.A.DP..KPMIIGTNN.FEVGCYSQAMK.MG..NVI.SKAYV..NVILTSGCI..ACC.LNTFEVIPEN
Retrocopy PNADDPDLKPMIIGTNNDFEVGCYSQAMK>MGNHNVIVSKAYVE*NVILTSGCITVACCNLNTFEVIPEN

Parental  TVIYGAD
          TVI.GAD
Retrocopy TVIDGAD

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	31.88 RPM
SRP017611_brain	0.00 RPM	25.96 RPM
SRP017611_kidney	0.00 RPM	49.46 RPM
SRP017611_liver	0.00 RPM	6.45 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2154 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2154 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2154 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001497	1 retrocopy	retro_amel_1860,
Canis familiaris	ENSCAFG00000006518	1 retrocopy	retro_cfam_2154 ,
Choloepus hoffmanni	ENSCHOG00000002554	3 retrocopies	retro_chof_1387, retro_chof_390, retro_chof_71,
Cavia porcellus	ENSCPOG00000011021	2 retrocopies	retro_cpor_1437, retro_cpor_706,
Echinops telfairi	ENSETEG00000012307	2 retrocopies	retro_etel_1571, retro_etel_1652,
Felis catus	ENSFCAG00000000133	1 retrocopy	retro_fcat_113,
Homo sapiens	ENSG00000104671	1 retrocopy	retro_hsap_1780,
Gorilla gorilla	ENSGGOG00000013074	1 retrocopy	retro_ggor_2236,
Myotis lucifugus	ENSMLUG00000028330	2 retrocopies	retro_mluc_1616, retro_mluc_2026,
Macaca mulatta	ENSMMUG00000013735	1 retrocopy	retro_mmul_1241,
Monodelphis domestica	ENSMODG00000019010	1 retrocopy	retro_mdom_1260,
Nomascus leucogenys	ENSNLEG00000011906	2 retrocopies	retro_nleu_1311, retro_nleu_2969,
Oryctolagus cuniculus	ENSOCUG00000010968	1 retrocopy	retro_ocun_917,
Ochotona princeps	ENSOPRG00000005061	1 retrocopy	retro_opri_950,
Pan troglodytes	ENSPTRG00000020134	1 retrocopy	retro_ptro_1191,
Tarsius syrichta	ENSTSYG00000013306	1 retrocopy	retro_tsyr_893,
Tursiops truncatus	ENSTTRG00000012439	1 retrocopy	retro_ttru_780,