RetrogeneDB ID: retro_cfam_1759

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:32458291..32459455(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR12
• Ensembl ID: ENSCAFG00000012519
• Aliases: None
• Description: WD repeat domain 12 [Source:HGNC Symbol;Acc:14098]

Sequence

>retro_cfam_1759
ATGGCTCAGCTCCAGACACGCTTCTTCACTGACAACAAGAAATATGTGGTAGATGATGTACCCTTCTCAATTTCTGCAGC
CTCTGAAATTGCTGACCTTAGTAACATCATCAGTAAATTGCTGGAGGCCAAAAATTAGTTCCACAAACATGTGGAGTTCG
ATTTCCTTATCAAGGGCCAGTTTCTCTGGTTGCCCTTACTCAAACACATGGAACTGGAAAACATCTCATCAGAAGAGGTT
GTGGAACTGGAATATGTGGAGAAGTACACTGCACCTCAGCCAGAGCAATGCTTGTTCCACGATGACTGGATCAGTTCAGT
CAGAGGGGCAGAGGAATGGATCTTGACTGGTTCTTATGATAAGACTTCTCAGATCTGGTCCTTGGAAGGAAAGTCAATAA
TGACAATTGTGGGACATACAGATGTTGTAAAAGATGTGGCCTGGGTGAAAAAAGATAATTTGTCTTGCCTACTACTGAGT
TCCTTTATGGATCAAACTATTCTCTTATGGGAGTGGAATGTGGAGAGAAACAAAGTGAAAGCTTTGCACTGCTGCAGAGG
TCATGCTGGAAGTGTGGGTTCTATAGCTATTGATAGCATGGGAACTAAATTTTGCAGTGGATCCTGGGATAAGATGCTAA
AGATCTGGTCTACAGTTCCTACAGATGAAGAGGATGAAATAGAGGAGCCCACAAATCGACCGAGAAAGAAACAGAAAACG
GAACAGTTGGGACTGACAAGGACTCCTATAGTGACCCTCTTGGCCACAAGGAAGCAATTTCCTGGGTTCTGTGGTCAGAT
GCTGAAGAAACCTGCAGTGGGTCTTGGGACCACAAAATTAGAGTATGGGATATAGAGTCTGGCAGTCTTAAGTCAACTCT
GACAGCAAATAAAGTGTTTAATTGTATCTCCTATTCTCCACTTTGTAAACGTTTGGCATCTGGAAACACAGATAGATATA
CCAGACCATGAGATCCCCCGAACTAAAGATGGTTCTTTGGTGTCGCTGTCCCTGACCTCACATACGGGCTGGGTCACATC
ATTAAAGTGGTCTCCTACCCATGAGCAGCAGCTGATTTCAGGCTCTTTAGATAACATTGTCAAACTGTGGGATACAAGAA
GTTGTAAGGCTCCTCTCTATGATCTGGCTGCTCATGAAGACAAA

Alignment

ORF - retro_cfam_1759 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.59 %
• Parental protein coverage: 91.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAQLQTRFFTDNKKYVVDDVPFSIPAASEIADLSNIINKLLEAKNEFHKHVEFDFLIKGQFLRLPLLKHM
          MAQLQTRFFTDNKKYVVDDVPFSI.AASEIADLSNII.KLLEAKN.FHKHVEFDFLIKGQFL.LPLLKHM
Retrocopy MAQLQTRFFTDNKKYVVDDVPFSISAASEIADLSNIISKLLEAKN*FHKHVEFDFLIKGQFLWLPLLKHM

Parental  ELENISSEEVVELEYVEKYTAPQPEQCLFHDDWISSVRGAEEWILTGSYDKTSRIWSLEGKSIMTIVGHT
          ELENISSEEVVELEYVEKYTAPQPEQCLFHDDWISSVRGAEEWILTGSYDKTS.IWSLEGKSIMTIVGHT
Retrocopy ELENISSEEVVELEYVEKYTAPQPEQCLFHDDWISSVRGAEEWILTGSYDKTSQIWSLEGKSIMTIVGHT

Parental  DVVKDVAWVKKDNLSCLLLSSSMDQTILLWEWNVERNKVKALHCCRGHAGSVDSIAVDSTGTKFCSGSWD
          DVVKDVAWVKKDNLSCLLLSS.MDQTILLWEWNVERNKVKALHCCRGHAGSV.SIA.DS.GTKFCSGSWD
Retrocopy DVVKDVAWVKKDNLSCLLLSSFMDQTILLWEWNVERNKVKALHCCRGHAGSVGSIAIDSMGTKFCSGSWD

Parental  KMLKIWSAVPTDEEDELEEPTNRPRKKQKTEQLGLTRTPIVTL-SGHKEAISSVLWSDAEEICSASWDHT
          KMLKIWS.VPTDEEDE.EEPTNRPRKKQKTEQLGLTRTPIVTL..GHKEAIS.VLWSDAEE.CS.SWDH.
Retrocopy KMLKIWSTVPTDEEDEIEEPTNRPRKKQKTEQLGLTRTPIVTL<LGHKEAISWVLWSDAEETCSGSWDHK

Parental  IRVWDVESGSLKSTLTGNKVFNCISYSPLCKRLASGSTDRHIRLWD-PRTKDGSLVSLSLTSHTGWVTSL
          IRVWD.ESGSLKSTLT.NKVFNCISYSPLCKRLASG.TDR..R..D.PRTKDGSLVSLSLTSHTGWVTSL
Retrocopy IRVWDIESGSLKSTLTANKVFNCISYSPLCKRLASGNTDRYTRP*D>PRTKDGSLVSLSLTSHTGWVTSL

Parental  KWSPTHEQQLISGSLDNIVKLWDTRSCKAPLYDLAAHEDK
          KWSPTHEQQLISGSLDNIVKLWDTRSCKAPLYDLAAHEDK
Retrocopy KWSPTHEQQLISGSLDNIVKLWDTRSCKAPLYDLAAHEDK

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	0.08 RPM	20.37 RPM
SRP017611_brain	0.08 RPM	18.10 RPM
SRP017611_kidney	0.07 RPM	9.91 RPM
SRP017611_liver	0.00 RPM	3.48 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1759 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1759 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1759 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012519	1 retrocopy	retro_cfam_1759 ,
Choloepus hoffmanni	ENSCHOG00000013851	1 retrocopy	retro_chof_118,
Callithrix jacchus	ENSCJAG00000005171	1 retrocopy	retro_cjac_2690,
Cavia porcellus	ENSCPOG00000008824	1 retrocopy	retro_cpor_1107,
Homo sapiens	ENSG00000138442	1 retrocopy	retro_hsap_1615,
Gorilla gorilla	ENSGGOG00000026073	1 retrocopy	retro_ggor_1222,
Loxodonta africana	ENSLAFG00000011955	1 retrocopy	retro_lafr_1102,
Mus musculus	ENSMUSG00000026019	3 retrocopies	retro_mmus_1394, retro_mmus_2649, retro_mmus_2897,
Nomascus leucogenys	ENSNLEG00000007018	1 retrocopy	retro_nleu_2743,
Pongo abelii	ENSPPYG00000013089	1 retrocopy	retro_pabe_1327,
Pan troglodytes	ENSPTRG00000012823	1 retrocopy	retro_ptro_1083,
Tursiops truncatus	ENSTTRG00000001231	1 retrocopy	retro_ttru_1380,