RetrogeneDB ID: retro_cfam_910

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:79209907..79210815(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000015166
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: WDR61
• Ensembl ID: ENSCAFG00000014230
• Aliases: None
• Description: WD repeat domain 61 [Source:HGNC Symbol;Acc:30300]

Sequence

>retro_cfam_910
ATGATCAACCAGTACAGTATTCTCTTCAAACAAGAACAAGCCCGTGATGATGCCATTTGGTCAGTTGCCTGGGGGACAAA
CAAGAAAGAAAACTCTGAGACGGTGGTTATGGGGTCCCTGGATGACCTGGTGAAGGTCTGGAAGTGGTGTGATGAGAGGC
TGAACCTACAGTGGAGTCTAGAGGGACATCAACTGGGCAGGGTGTCTGTGGACATCAGCCACACGCTGCCCATCGCTGTG
TCCAGTTCTCTTGACGCTCATATTCGTCCCTGGACTTGGATAACGGCAAACAGATAAAATCTAAAGATGCAGTGGATGCC
TGGACTTTGGCCTTTTCTCCTGATTCCCAGTATCTGGCCACAGGAACTCATGTGGGTAAAGTGAACATTTTTGGTGTGGA
AAGTGGGAAAAAGGAATATTCTCTGGACACGAGAGGAAAATTCATTGTTAGTATTGCATATAGCCGTGATGGGAAGTATC
TGGCCAGTGGAGCCATAGATGGGATCATCAATATTTTTGATATTGCAACTGGAAGACTTCTGCACACCCTGGAAGGCCGT
GCTATGCCTATCTGTTCCCTGACATTCTCCCCAGGTTCTCAGCTCCTGGTCCCTGCATCAGATGATGGCTACATCAAGGT
CTTTGATGTACAACATGCCAATTTGGCTGGCACACTGAGTGGCCATGCATCATGGGTGTTGAATGTTGTGTTTTGTCCTG
ACGACACTCACATTGTGTCCAGTTCATCTGATAAAAGTGTGAAAGTTTGGGATGTTGGAACAAGAACCTGTGTTCACACC
TTCTTCGATCACCAGGATCAGGTGTGGGGAGTAAAATACAATGGAAATCGCTCAAAGATTATGTCCATGGGTGATGACCA
GGAAATCCATGTCTATGATTGCCCCGTA

Alignment

ORF - retro_cfam_910 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTNQYSILFKQEQAHDDAIWSVAWGTNKKENSETVVTGSLDDLVKVWKWCDERLDLQWSLEGHQLGVVSV
          M.NQYSILFKQEQA.DDAIWSVAWGTNKKENSETVV.GSLDDLVKVWKWCDERL.LQWSLEGHQLG.VSV
Retrocopy MINQYSILFKQEQARDDAIWSVAWGTNKKENSETVVMGSLDDLVKVWKWCDERLNLQWSLEGHQLGRVSV

Parental  DISHTLPIAASSSLDAHIRLW-DLDNGKQIKSIDAGPVDAWTLAFSPDSQYLATGTHVGKVNIFGVESGK
          DISHTLPIA.SSSLDAHIR.W.DLDNGKQIKS.DA..VDAWTLAFSPDSQYLATGTHVGKVNIFGVESGK
Retrocopy DISHTLPIAVSSSLDAHIRPW<DLDNGKQIKSKDA--VDAWTLAFSPDSQYLATGTHVGKVNIFGVESGK

Parental  KEYSLDTRGKFILSIAYSPDGKYLASGAIDGIINIFDIATGKLLHTLEGHAMPIRSLTFSPDSQLLVTAS
          KEYSLDTRGKFI.SIAYS.DGKYLASGAIDGIINIFDIATG.LLHTLEG.AMPI.SLTFSP.SQLLV.AS
Retrocopy KEYSLDTRGKFIVSIAYSRDGKYLASGAIDGIINIFDIATGRLLHTLEGRAMPICSLTFSPGSQLLVPAS

Parental  DDGYIKIYDVQHANLAGTLSGHASWVLNVAFCPDDTHFVSSSSDKSVKVWDVGTRTCVHTFFDHQDQVWG
          DDGYIK..DVQHANLAGTLSGHASWVLNV.FCPDDTH.VSSSSDKSVKVWDVGTRTCVHTFFDHQDQVWG
Retrocopy DDGYIKVFDVQHANLAGTLSGHASWVLNVVFCPDDTHIVSSSSDKSVKVWDVGTRTCVHTFFDHQDQVWG

Parental  VKYNGNGSKIVSVGDDQEIHVYDCPV
          VKYNGN.SKI.S.GDDQEIHVYDCPV
Retrocopy VKYNGNRSKIMSMGDDQEIHVYDCPV

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	1.64 RPM	31.37 RPM
SRP017611_brain	0.40 RPM	24.29 RPM
SRP017611_kidney	1.32 RPM	63.73 RPM
SRP017611_liver	0.00 RPM	15.45 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_910 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_910 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_910 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014230	3 retrocopies	retro_cfam_1378, retro_cfam_1422, retro_cfam_910 ,
Macropus eugenii	ENSMEUG00000015991	1 retrocopy	retro_meug_744,
Oryctolagus cuniculus	ENSOCUG00000009040	1 retrocopy	retro_ocun_1570,
Ictidomys tridecemlineatus	ENSSTOG00000007784	1 retrocopy	retro_itri_843,
Tupaia belangeri	ENSTBEG00000009390	1 retrocopy	retro_tbel_48,