RetrogeneDB ID: retro_cfam_865

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:17679574..17680108(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000031711
• Aliases: None
• Description: None

Sequence

>retro_cfam_865
GCCAGGGGGCCATTCCTGTGAGCAATACTGTCAGATTCTTAGGCAGTCCTGCCCACCAGTGGGGGACTACAGATGCTGCT
CCCAGTGGCAACTTCTGAAGATGTTTCCGTTCCTGAAAAGCCTCAGCTTAGATTTGTTGAAAGGGCACCACTTGTGCCAA
AAGTGGGAAGAGAATCTAAAACCTTGGGTGACATATGGGGACCTTTACTGAAGCTACTGAGTTCACTGAAGGCAATTTTG
CAATCTTGGCACTTGGTGGTGGTTACCTCCATTGGGACCATTTTAAAATGATGTACCTGACAATGAGCTGCTCTGCGGAC
CCCAAGAACATGTTTGCCTTATGGAGAGTACCACCTCCTTTCAGGCCTATCACCTGCAAGGGTATGAGACAGTAAGTGGG
GGGAGGCAAAAGTGCTTTTGGTCACAATATGACTCCTTGTGAAGGCTGGCTATCTCATAATAGAGATGAGTGGGAATTGT
GAATTCAAAGAGATACAAGGTTTCCTTGACTATATTGCTCACAAATTGCCCTTC

Alignment

ORF - retro_cfam_865 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.89 %
• Parental protein coverage: 70.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGAPLLRARTSGPRAAPPARAGLKTLLPVPTFEDVSIPEKPKLRFVERVPLVPKVRREPKNLSDIRGPS-
          A..P.L.A..S...A..P...GL..LLPV.T.EDVS.PEKP.LRFVER.PLVPKV.RE.K.L.DI.GP..
Retrocopy ARGPFL*AILSDS*AVLPTSGGLQMLLPVATSEDVSVPEKPQLRFVERAPLVPKVGRESKTLGDIWGPL<

Parental  TEATEFTEGNFAILALGGGYLHWGHFEMMRLTINRSMDPKNMFALWRVPAPFKPITRKGVGQRMGGGKGA
          TEATEFTEGNFAILALGGGYLHW.HF.MM.LT...S.DPKNMFALWRVP.PF.PIT.KG..Q..GGGK.A
Retrocopy TEATEFTEGNFAILALGGGYLHWDHFKMMYLTMSCSADPKNMFALWRVPPPFRPITCKGMRQ*VGGGKSA

Parental  IDHYVTP-VKAGRLIVELGGRCEFKEVQGFLDQVAHKLPF
          ..H..TP.VKAG.LI.E..G.CEFKE.QGFLD..AHKLPF
Retrocopy FGHNMTP>VKAGYLIIEMSGNCEFKEIQGFLDYIAHKLPF

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	1.09 RPM
SRP017611_brain	0.00 RPM	0.71 RPM
SRP017611_kidney	0.00 RPM	0.86 RPM
SRP017611_liver	0.00 RPM	0.44 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_865 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_865 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_865 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014289	1 retrocopy	retro_amel_1231,
Canis familiaris	ENSCAFG00000031711	2 retrocopies	retro_cfam_393, retro_cfam_865 ,
Dipodomys ordii	ENSDORG00000015111	1 retrocopy	retro_dord_389,
Felis catus	ENSFCAG00000007540	2 retrocopies	retro_fcat_479, retro_fcat_639,