RetrogeneDB ID: retro_cfam_1264

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 28:12481874..12482774(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARMC10
• Ensembl ID: ENSCAFG00000004247
• Aliases: None
• Description: armadillo repeat containing 10 [Source:HGNC Symbol;Acc:21706]

Sequence

>retro_cfam_1264
AGCATGGGTGGCGCCTGGGACGTGGGCTGGGTGGCCGAGGGCCTGGTCCTCCGGGCCAGTGCCTGCTACTGCATTTACAA
GCTGATGCGGGGCTGGTGGTGAGGCACCCACGGGCTTCGGCTGCGCCCCTCGCACTCCGTAGAAGACTTAACCAGTGGTT
CACATGATGATGTCCTAAATGTTGACCAGCTCCAGAAACTCCTCTACCTGCTTGAGTCAACTGATGATCCTGTAATTATT
TAAAGAGCTTTGGTCACTCTGGGTAACAATGCAGGCTTTTCAGCTAACCAAGTCATTATACGTGAATTGGGTGGTATTCC
AATCATTGAAAGCAAAATCAACAATCCCAACCACAGCCTTAAAGAGAAAGCTTAAAATGCATTGAATAACCTGAGTGTGA
ATCTTGAAAATCAAGTCAAGATAAAGGTATACATCAATCAAGTCTGTAAGGATGTCCTCTTTGGTCCCCTGGACTCTGCA
GTGCAGCTGGCTGGGCTGAGACTGTTAACAAACATGACCGTGACTAACAACCACCAGCACATGCTTACTGATTACATCAC
AGACCTGTTACTCACAGGGGATGGAAGTACCATGGTTCAAGTTTTGAAACTCCTTGTAAATTTGTCTGAAAATCCAGCCA
TGACAAAAGTACTACTTGGTTCCCAAATGGATTCCTCATTCCTTTCCCTTTATGACCACCACGTGGCAAAGGAGATTCTT
CTTCGAGTCCTGACGCTATCTCAAAATATAAACAACTGTTTCGAAAAAGGTTCTTTAGCTGTTCAGCCTACTTTCCCTAA
AGGTTCCCTGTTTTTCCTGTTATATGGAAAATAATGTGCCCAGAAAATGAGGGCTTTAGCCAAACACCATGATGCAGATG
TGAAGGAAAAGGTCATAGTC

Alignment

ORF - retro_cfam_1264 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.46 %
• Parental protein coverage: 64.61 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SMGGARDVGWVAAGLVLGAGACYYIYKLARGRRRGARGLRLRPSRSAEDLTNGSYDDVLNVDQLQKLLYL
          SMGGA.DVGWVA.GLVL.A.ACY.IYKL.RG...G..GLRLRPS.S.EDLT.GS.DDVLNVDQLQKLLYL
Retrocopy SMGGAWDVGWVAEGLVLRASACYCIYKLMRGWW*GTHGLRLRPSHSVEDLTSGSHDDVLNVDQLQKLLYL

Parental  LESTDDPVIIERALVTLGNNAAFSANQVIIRELGGIPIIGSKINNPNHSIKEKALNALNNLSVNVENQVK
          LESTDDPVII.RALVTLGNNA.FSANQVIIRELGGIPII.SKINNPNHS.KEKA.NALNNLSVN.ENQVK
Retrocopy LESTDDPVII*RALVTLGNNAGFSANQVIIRELGGIPIIESKINNPNHSLKEKA*NALNNLSVNLENQVK

Parental  IKVYINQVCKDVLSGPLDSAVQLAGLRLLTNMTVTNDHQHMLTDYVTDLFHVLLTGDGSTKVQVLKLLVN
          IKVYINQVCKDVL.GPLDSAVQLAGLRLLTNMTVTN.HQHMLTDY.TDL...LLTGDGST.VQVLKLLVN
Retrocopy IKVYINQVCKDVLFGPLDSAVQLAGLRLLTNMTVTNNHQHMLTDYITDL---LLTGDGSTMVQVLKLLVN

Parental  LSENPAMTEVLLGAQVDSSFVSLYDGHVAKEILLRVLTLSQNINNCLEKGSLAVQPTFPKGSLFFLLYGE
          LSENPAMT.VLLG.Q.DSSF.SLYD.HVAKEILLRVLTLSQNINNC.EKGSLAVQPTFPKGSLFFLLYG.
Retrocopy LSENPAMTKVLLGSQMDSSFLSLYDHHVAKEILLRVLTLSQNINNCFEKGSLAVQPTFPKGSLFFLLYGK

Parental  ECAQKMRALAKHHDADVKEKIDV
          .CAQKMRALAKHHDADVKEK..V
Retrocopy *CAQKMRALAKHHDADVKEKVIV

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	17.93 RPM
SRP017611_brain	0.00 RPM	18.42 RPM
SRP017611_kidney	0.00 RPM	12.08 RPM
SRP017611_liver	0.00 RPM	3.70 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1264 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1264 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1264 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004247	1 retrocopy	retro_cfam_1264 ,
Choloepus hoffmanni	ENSCHOG00000002095	1 retrocopy	retro_chof_2665,
Callithrix jacchus	ENSCJAG00000021208	2 retrocopies	retro_cjac_1758, retro_cjac_2104,
Cavia porcellus	ENSCPOG00000019936	1 retrocopy	retro_cpor_1022,
Homo sapiens	ENSG00000170632	1 retrocopy	retro_hsap_2815,
Microcebus murinus	ENSMICG00000010160	1 retrocopy	retro_mmur_638,
Myotis lucifugus	ENSMLUG00000006088	3 retrocopies	retro_mluc_1587, retro_mluc_1825, retro_mluc_624,
Mus musculus	ENSMUSG00000038525	3 retrocopies	retro_mmus_1292, retro_mmus_2256, retro_mmus_969,
Vicugna pacos	ENSVPAG00000008914	1 retrocopy	retro_vpac_19,