RetrogeneDB ID: retro_cfam_1713

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:78878973..78879765(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EHD1
• Ensembl ID: ENSCAFG00000014128
• Aliases: None
• Description: EH-domain containing 1 [Source:HGNC Symbol;Acc:3242]

Sequence

>retro_cfam_1713
CCCATGCTACTTCTCGTGGGCTAGTGCAGCACTGGCAAGACCACCTTCATCTGGCCCCTGATCCAACAGGCCTTCCCAGG
AGTTGGCATCTGGCCTTGCACACCACTGATGCCTTCATTTCCCAGGGGCACAGCCTCACCAAGGGCCTGGTGCCTGGCCA
CATGCTTGGGTGGATGCATGGAGCCCCATCTGCCAGCTCAACGAAGTTGGGCAACAGGTTCCTCAGCAGGTTCACAGGTG
CCTCCCACCCATCCCAGTGTAGGACAGCATATGCATCACAGACACTCCCGGGATGCTGTCTTGAGAGAAGTAGGGCATCA
GCAGAGGTTATGGCTGGGGGTGGTCCTGGAGTAGTTGGCTGAATGTATCTACCGCATTGTACCATTTTTTGAGACCATTT
GGTGGACACCTTTGAAGAGTTCTCCTAAGTCATCATGGCCCTGAAAAACCAGAAGGACAAGATATGGGGGATGGTGAACA
AGAGCTACCCAACAGAGACCCATCAGCCCGTCTTGGGGGTGGGGTTGTAGTCTCTGGGAAAGATCAACCCCCCTGAGGTG
GTCAGCTGCTTCTGCTTCCACCTGCTTCTAATCTCTGACATCCATGGGCTCTCCTAGGCTGAGGAGCAGGGCCTGCTAAA
AGACATCCAGTCTCTGCCCCCAAATACTGTCCTCAAAAAACTCAGTGAATTAAACAAGTGGGTATGGCTGGCCAACATCC
ATGCCTACCTACATCATTAGCTCCCTTAAGGAGGAAGTGTTCAATGTCTTCAGTAAACAGAGCAAAAAGAAA

Alignment

ORF - retro_cfam_1713 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.26 %
• Parental protein coverage: 57.54 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PMVLLVGQYSTGKTTFIRHLIEQDFPGMRIGPEP-TTDSFIAVMHGPTEGVVPGNALVVDPRRPFRKLNA
          PM.LLVG..STGKTTFI..LI.Q.FPG..I.P...TTD.FI...H..T.G.VPG..L......P......
Retrocopy PMLLLVG*CSTGKTTFIWPLIQQAFPGVGIWPCT<TTDAFISQGHSLTKGLVPGHMLGWMHGAPSASSTK

Parental  FGNAFLNRFMCAQLPN-PVLDSISIIDTPGILSGEKQRISRGYDFA-AVLEWFAERVDRIILLFDA-HKL
          .GN.FL.RF..A..P..PV.DSI.I.DTPG.LS.EK..ISRGY.....VLE..AE...RI...F...H..
Retrocopy LGNRFLSRFTGASHPS<PV*DSICITDTPGMLS*EK*GISRGYGWG<VVLE*LAECIYRIVPFFET<HLV

Parental  DISDEFSEVIKALKNHEDKIRVVLNKADQIETQQLMRVYGALMWSLGKIINTPEVVRVYIGSFWSHPLLI
          D...EFS.VI.ALKN..DKI....NK....ET.Q...V.G....SLGKI.N.PEV.......F..H.LLI
Retrocopy DTFEEFS*VIMALKNQKDKIWGMVNKSYPTETHQ--PVLGVGL*SLGKI-NPPEV----VSCFCFHLLLI

Parental  PDNRKLFEAEEQDLFKDIQSLPRNAALRKLNDLIKRARLAKVHAYI-ISSLKKE-MPNVFGKESKKK
          .D...L..AEEQ.L.KDIQSLP.N..L.KL..L.K...LA..HAY..I.S..KE...NVF.K.SKKK
Retrocopy SDIHGLS*AEEQGLLKDIQSLPPNTVLKKLSELNKWVWLANIHAYL>IISSLKEEVFNVFSKQSKKK

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	68.50 RPM
SRP017611_brain	0.00 RPM	35.25 RPM
SRP017611_kidney	0.00 RPM	64.91 RPM
SRP017611_liver	0.00 RPM	29.37 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1713 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1713 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1713 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014128	1 retrocopy	retro_cfam_1713 ,
Callithrix jacchus	ENSCJAG00000002660	1 retrocopy	retro_cjac_559,
Sarcophilus harrisii	ENSSHAG00000005706	1 retrocopy	retro_shar_423,