RetrogeneDB ID: retro_cfam_343

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:6922243..6922709(+)
• Located in intron of: ENSCAFG00000000345

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD1
• Ensembl ID: ENSCAFG00000003090
• Aliases: None
• Description: Canis lupus familiaris copper metabolism (Murr1) domain containing 1 (COMMD1), mRNA. [Source:RefSeq mRNA;Acc:NM_001003055]

Sequence

>retro_cfam_343
GGCGAGCTGGCTCCGAAGCTCCAGCGAGCTGCTGAGCAGTGGCAGCCGCACATCACAGAGGAGCTGCTATGGGGCCAGCT
CTATCCAGAGGTGTCCCCTGAGGAGCTCTGCCCCTTGCTGGCGAACATGAGGGGGATCCTTACGTCTGTTGTATCTGTTG
CATCAGCAGACATGGATTTCAACCAGCCAGAGGTGTTCTTGACAGCTCAGAAACCAAAAAGCAAGGTGGGATCACTTCTG
ACCAAGCTGCCATCATTTCCAAATTCTGGAAGACCCATAAGATAGAAATTCGAGAGAGCCCCATGAACCAGAGCCATTGG
GACTGTAGGCTGGGGGCCTGAGCTGCAGAGTTCATGGCAAATCCCAGGCAAGGCACTCGGCTCATGTGCACACCCCTCTT
GCCATAATGGGGCTGGAAATAGGGAAAAGTGGCCTGGAAACTGAATTTCTCTGTTTGGCATTTGAC

Alignment

ORF - retro_cfam_343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.66 %
• Parental protein coverage: 80.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGLLSGLAQEAFHGHQGITEELLRSQLYPEVSLEEFRPFLAKMRGILKS---IASADMDFNQLEAFLTAQ
          G.L...L...A......ITEELL..QLYPEVS.EE..P.LA.MRGIL.S....ASADMDFNQ.E.FLTAQ
Retrocopy GELAPKLQRAAEQWQPHITEELLWGQLYPEVSPEELCPLLANMRGILTSVVSVASADMDFNQPEVFLTAQ

Parental  -TKKQGGITSDQAAVI-SKFWKNHKTKIRESLMNQSRWDSGL-RGLSWRVDGKSQSRHSAQIHTPVAIME
          ...K..G......A.I.SKFWK.HK..IRES.MNQS.WD..L..GLS.RV.GKSQ.RHSA..HTP.AIM.
Retrocopy <ETKKQGGITSDQAAIISKFWKTHKIEIRESPMNQSHWDCRL<GGLSCRVHGKSQARHSAHVHTPLAIMG

Parental  LEIGKSGQESEFLCLEFD
          LEIGKSG.E.EFLCL.FD
Retrocopy LEIGKSGLETEFLCLAFD

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	59.01 RPM
SRP017611_brain	0.00 RPM	42.71 RPM
SRP017611_kidney	0.00 RPM	70.79 RPM
SRP017611_liver	0.00 RPM	17.77 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_343 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_343 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_343 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003090	1 retrocopy	retro_cfam_343 ,
Cavia porcellus	ENSCPOG00000002088	1 retrocopy	retro_cpor_482,
Mustela putorius furo	ENSMPUG00000005842	1 retrocopy	retro_mputfur_1120,
Ictidomys tridecemlineatus	ENSSTOG00000015062	1 retrocopy	retro_itri_562,
Tarsius syrichta	ENSTSYG00000000812	1 retrocopy	retro_tsyr_88,