RetrogeneDB ID: retro_cfam_1852

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:39271123..39271666(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM221A
• Ensembl ID: ENSCAFG00000002784
• Aliases: FAM221A, C14H7orf46
• Description: family with sequence similarity 221, member A [Source:HGNC Symbol;Acc:27977]

Sequence

>retro_cfam_1852
GGGATGCGGCCCATTCGCTGCAGGTGCAAGCACTTTGTGGCTCAGCACAGCACTGCGCCAGGCTTTATATGCAACGTCTG
TTCCAAGTGTTCAGGATTCCATAGTTGCTTCGCTTGTGCTTGCGGTCAGCCTGCATATGCTCATGACACAGTAGTGGAAC
CTAAGCACCAAAGACTGGCTCAGGGCAAACCAGTGGGACAGGATGTTCCTTGTGCAGCGATGGGAGGCTGAACTGGCTTC
AGCCCACTGGCAGAAGGCTACGTGCGATGAGATGACAGTGGGCTTGGTGCGCCTTCAATTGGACTTTTAGACTCTCCGGT
TACAGCCATGGACCACCCATTTCTAACAGCATTACAAGCATCATCTCGTTCTTCTCCAGGAACACGGACAGATGTAGGTA
CGAGTAGCCAAGTTTCCTCCATAAAGAGACCTGCGGAGGATGACACGGCTTTCTTTGAAAGACAATACCAAGAAAAGATA
AAGATGAAAAAGGTTGCTAAGAAGAAAGGAAAGGCACCATTGCCATCAAGTACAAAAGCTTCA

Alignment

ORF - retro_cfam_1852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.22 %
• Parental protein coverage: 72.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTQPIRCRCKHFADQHSPAAGFICNVCSKCSGFHSCFTCACGQPAYAHDTVVETKQERLAQGKPVGQDVP
          G..PIRCRCKHF..QHS.A.GFICNVCSKCSGFHSCF.CACGQPAYAHDTVVE.K..RLAQGKPVGQDVP
Retrocopy GMRPIRCRCKHFVAQHSTAPGFICNVCSKCSGFHSCFACACGQPAYAHDTVVEPKHQRLAQGKPVGQDVP

Parental  YAAMGGLTGFSSLAEGYMRLDDSGTGAPSIEFLDSPVTTMDHPFLKSFQASSSSSPETLRDAGTSSQVSS
          .AAMGG.TGFS.LAEGY.R.DDSG.GAPSI..LDSPVT.MDHPFL...QASS.SSP.T..D.GTSSQVSS
Retrocopy CAAMGG*TGFSPLAEGYVR*DDSGLGAPSIGLLDSPVTAMDHPFLTALQASSRSSPGTRTDVGTSSQVSS

Parental  IKRPEEDDMAFFERRYQERIKMEKVAKQKGKAPLPSSTKPS
          IKRP.EDD.AFFER.YQE.IKM.KVAK.KGKAPLPSSTK.S
Retrocopy IKRPAEDDTAFFERQYQEKIKMKKVAKKKGKAPLPSSTKAS

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	3.36 RPM
SRP017611_brain	0.00 RPM	2.38 RPM
SRP017611_kidney	0.00 RPM	11.29 RPM
SRP017611_liver	0.07 RPM	0.80 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1852 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1852 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1852 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002784	1 retrocopy	retro_cfam_1852 ,
Erinaceus europaeus	ENSEEUG00000001634	2 retrocopies	retro_eeur_349, retro_eeur_397,