RetrogeneDB ID: retro_cfam_1424

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 30:36941035..36941517(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZMAT5
• Ensembl ID: ENSCAFG00000012343
• Aliases: None
• Description: zinc finger, matrin-type 5 [Source:HGNC Symbol;Acc:28046]

Sequence

>retro_cfam_1424
GGGTAGCATTAGTTCTTTGACTACTGCAACAGCTCTTTCCAGGACAACCTCCCCAACCACAGGAAGCTCCTGCAGCACCT
GAAGGCCAGGAAGGTCTGGTATGACATGTTCCAAGATGCAGCTGCCATCTTGCTAATGAACAGAATGAGTGGCCCTACAG
GTAATTTCTACTGACAGGCCAGTGTGACTCTGCCTCCAACTGCAAACTTTCCCACATGTCAGCGACAGACCTGCAGGAGC
TGAGTATCCAGGTGGAGGAGGAGAGGCGGGCCAGGGAGTGGCCACTAGATGTCACAGAGCTCCCTAAGGGCCATCTGGAA
GACTGGTTGGAAAAGAGAGCCAAGGCGCCAAGCTGCAGGGCTGAATCCATGAGAACCACTATCTTCCAGTATCCCATAGA
CTGACCACCGGGGCAAAGGTTGCCTCAATTCCTGAAGGTACCCCCTCACAGGGGCTGGCCCCTTCAGCCCAGCATCATCT
GG

Alignment

ORF - retro_cfam_1424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.78 %
• Parental protein coverage: 98.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKHYFCDYCNRSFQDNLHNRKKHLNGLQHLKAKKVWYDMFRDAAAILL-DEQNKRPCRKFLLTGQCDFGS
          G.H.F.DYCN.SFQDNL.N..K....LQHLKA.KVWYDMF.DAAAILL..EQN..P.R.FLLTGQCD..S
Retrocopy G*H*FFDYCNSSFQDNLPNHRKL---LQHLKARKVWYDMFQDAAAILL<NEQNEWPYR*FLLTGQCDSAS

Parental  NCRFSHMSERDLQELSIQVEEERRAREWPLDVVELPEGHLEDWLEKRAKRLSSAPSSRAEPMRSTIFQYP
          NC..SHMS..DLQELSIQVEEERRAREWPLDV.ELP.GHLEDWLEKRAK....APS.RAE.MR.TIFQYP
Retrocopy NCKLSHMSATDLQELSIQVEEERRAREWPLDVTELPKGHLEDWLEKRAK----APSCRAESMRTTIFQYP

Parental  IGWPPVQELPPSLRAPPPGGWPLQPSVQW
          I..PP.Q.LP..L..PP..GWPLQPS..W
Retrocopy ID*PPGQRLPQFLKVPPHRGWPLQPSIIW

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	5.75 RPM
SRP017611_brain	0.00 RPM	5.16 RPM
SRP017611_kidney	0.00 RPM	6.60 RPM
SRP017611_liver	0.00 RPM	0.73 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1424 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1424 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1424 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008059	1 retrocopy	retro_amel_866,
Canis familiaris	ENSCAFG00000012343	2 retrocopies	retro_cfam_1130, retro_cfam_1424 ,
Cavia porcellus	ENSCPOG00000020994	1 retrocopy	retro_cpor_1043,
Echinops telfairi	ENSETEG00000003789	2 retrocopies	retro_etel_2098, retro_etel_421,
Felis catus	ENSFCAG00000004251	1 retrocopy	retro_fcat_824,
Myotis lucifugus	ENSMLUG00000017398	1 retrocopy	retro_mluc_568,
Mustela putorius furo	ENSMPUG00000013253	1 retrocopy	retro_mputfur_875,