RetrogeneDB ID: retro_cfam_1422

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 30:33084129..33085039(-)
• 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_1422
ATGACCAACCAGTACAGTATTCTCTTCAAACAAGAGCAAGCCCAGGATGATGCCATTTGGTCGGTTGCCTGGGGGACAAA
CAGAAAGAAAACTCTGAGATGGTGGTTACGGGGTCCCTGGATGACCTGGTGAAAGTCTAGAGGTGTTGTGATGAGAGGCT
GGACCTACAATGGAGTCTAGAGAGACATCAACTGGCCGTGGTGTCTGTGAACATCAGCCACACGCTGCCCATCGCTGCGT
CCAGTTCTCTTGACGCTCATATTCGTCTCTGGGACTTGGATAACAGCAAACAGATAAAATCTATAGATGCAGGACCAGTG
GATGCCTGGACTTTGGTTTTTTCTCCTGATCCCCAGTATCTGGCCACAGGAACTCATGTGGGGAAAGTGAACATTTTTGG
TGTGGAAAGTGGGAAAAAGAAATATTCTCTGGACACAAGAGGAAAATTCATTCTTAGTATTACATATAGCCCTGATGGGA
TGTATCTGACCAGTGGAGCCATAGATGGGGCCATCAATATTTTTGATATTGCAACTGGAAAACTTCTGCACACGCTGGAA
GGCCTTGCTATACCTATCCGTTCCCTGACATTCTCCCTGGCTTCTCAGCTCCTGGTCACTGCATCAGATGATGGCTACAT
CAAGATCTATGATGTACAACATGCCAATTTGGCTGGTACGCTGAGTGGCCATGCATCATGGGTGCTGAATGTTGCATTTT
GTCCTGACGACACCCACTTCGAGTCCAGTTCATCTGATATGTGAAAGTTTGGGATGTTGGAACAAGAACGTGTGTTCACA
CCTTCTTCGATCACCAGGATCAGGTCTGGGGAGTAAAATACAATGGAAATGGCTCAAAGATTGTGTCCATGGGTGATGAC
CAGGAAATCCACGTCTATGATTGCCCCGTG

Alignment

ORF - retro_cfam_1422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.55 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTNQYSILFKQEQAHDDAIWSVAWGTNKK-ENSETVVTGSLDDLVKVWKWCDERLDLQWSLEGHQLGVVS
          MTNQYSILFKQEQA.DDAIWSVAWGTN.K.ENSE.VVTGSLDDLVKV...CDERLDLQWSLE.HQL.VVS
Retrocopy MTNQYSILFKQEQAQDDAIWSVAWGTNRK<ENSEMVVTGSLDDLVKV*RCCDERLDLQWSLERHQLAVVS

Parental  VDISHTLPIAASSSLDAHIRLWDLDNGKQIKSIDAGPVDAWTLAFSPDSQYLATGTHVGKVNIFGVESGK
          V.ISHTLPIAASSSLDAHIRLWDLDN.KQIKSIDAGPVDAWTL.FSPD.QYLATGTHVGKVNIFGVESGK
Retrocopy VNISHTLPIAASSSLDAHIRLWDLDNSKQIKSIDAGPVDAWTLVFSPDPQYLATGTHVGKVNIFGVESGK

Parental  KEYSLDTRGKFILSIAYSPDGKYLASGAIDGIINIFDIATGKLLHTLEGHAMPIRSLTFSPDSQLLVTAS
          K.YSLDTRGKFILSI.YSPDG.YL.SGAIDG.INIFDIATGKLLHTLEG.A.PIRSLTFS..SQLLVTAS
Retrocopy KKYSLDTRGKFILSITYSPDGMYLTSGAIDGAINIFDIATGKLLHTLEGLAIPIRSLTFSLASQLLVTAS

Parental  DDGYIKIYDVQHANLAGTLSGHASWVLNVAFCPDDTHFVSSSSDKS-VKVWDVGTRTCVHTFFDHQDQVW
          DDGYIKIYDVQHANLAGTLSGHASWVLNVAFCPDDTHF..SSS....VKVWDVGTRTCVHTFFDHQDQVW
Retrocopy DDGYIKIYDVQHANLAGTLSGHASWVLNVAFCPDDTHF-ESSSSDM<VKVWDVGTRTCVHTFFDHQDQVW

Parental  GVKYNGNGSKIVSVGDDQEIHVYDCPV
          GVKYNGNGSKIVS.GDDQEIHVYDCPV
Retrocopy GVKYNGNGSKIVSMGDDQEIHVYDCPV

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	0.13 RPM	31.37 RPM
SRP017611_brain	0.00 RPM	24.29 RPM
SRP017611_kidney	0.13 RPM	63.73 RPM
SRP017611_liver	0.15 RPM	15.45 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1422 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1422 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1422 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,