RetrogeneDB ID: retro_cfam_1378

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:44576462..44577175(-)
• Located in intron of: None

Retrocopy information

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

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_1378
ATGTCTGTGGACATCAGCCACACGCTGCCCATCGCTGCGTCCAGTTCTCTTGATGCTCATATTCATCTCTGGGACTTGGA
TAACGGCAAACAGATAAAATCTATAGATGCAGGACCAGTGGATGCCTGGACTTTGGCCTTTTCTCCTGATTCCCAGTATC
TGGCCACAGGAACTCATGTGGGGAAAATGAACATTTTTGGTGTGGAAAGTGGGAAAAAGGAATATTCTCTGGACACAAGA
GGAAAATTCATTCTTAGTATTGCATATAGCTCTGATGGGAAGTATCTGGCCAGTGGATCCATGAATAGGATCATCAATAT
TTTGATATTGCAACTGGAAAACTTCTGCACACGCTGGGAGGCCATGCTATGCCTATCCGTTCCCTGATATTCTCCCCAGA
TTCTCAGCTCCTGGTCACTGCATCAGATGATAGCTACATCAAGATCTATGATGTACAACATGCCAATTTGGATGGCACGC
TGAATGGCCATGCATCATGGGTGCTGAATGTTGCGTTTTGTCCTGACGACACCCACTTTGTGTCCAGTTCATCTGATAAA
AGTGTGAAAGTTTGGGATGTTGGAACAAGAACCTGTGTTCACACCTTCTTCGATCACCAGGATCAGGTCTGGAGAGTAAA
ATACAATGGAAATGGCTTAAAGATTGTGTCCGTGGGTGATGACCAGGAAATCCACGTCTATGATTGCCCCGTG

Alignment

ORF - retro_cfam_1378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.31 %
• Parental protein coverage: 78.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSVDISHTLPIAASSSLDAHIRLWDLDNGKQIKSIDAGPVDAWTLAFSPDSQYLATGTHVGKVNIFGVES
          .SVDISHTLPIAASSSLDAHI.LWDLDNGKQIKSIDAGPVDAWTLAFSPDSQYLATGTHVGK.NIFGVES
Retrocopy MSVDISHTLPIAASSSLDAHIHLWDLDNGKQIKSIDAGPVDAWTLAFSPDSQYLATGTHVGKMNIFGVES

Parental  GKKEYSLDTRGKFILSIAYSPDGKYLASGAIDGIINI-FDIATGKLLHTLEGHAMPIRSLTFSPDSQLLV
          GKKEYSLDTRGKFILSIAYS.DGKYLASG....IINI.FDIATGKLLHTL.GHAMPIRSL.FSPDSQLLV
Retrocopy GKKEYSLDTRGKFILSIAYSSDGKYLASGSMNRIINI<FDIATGKLLHTLGGHAMPIRSLIFSPDSQLLV

Parental  TASDDGYIKIYDVQHANLAGTLSGHASWVLNVAFCPDDTHFVSSSSDKSVKVWDVGTRTCVHTFFDHQDQ
          TASDD.YIKIYDVQHANL.GTL.GHASWVLNVAFCPDDTHFVSSSSDKSVKVWDVGTRTCVHTFFDHQDQ
Retrocopy TASDDSYIKIYDVQHANLDGTLNGHASWVLNVAFCPDDTHFVSSSSDKSVKVWDVGTRTCVHTFFDHQDQ

Parental  VWGVKYNGNGSKIVSVGDDQEIHVYDCPV
          VW.VKYNGNG.KIVSVGDDQEIHVYDCPV
Retrocopy VWRVKYNGNGLKIVSVGDDQEIHVYDCPV

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	31.37 RPM
SRP017611_brain	0.00 RPM	24.29 RPM
SRP017611_kidney	0.00 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_1378 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1378 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1378 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,