RetrogeneDB ID: retro_cfam_1248

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:36566980..36567370(-)
• Located in intron of: ENSCAFG00000024781

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000000071
• Aliases: None
• Description: None

Sequence

>retro_cfam_1248
CTGGCCTACATCATCTTGGTAGGACTGCTGCATGTGGTTCTACTCAGCATCCCCTTCTTCAGCATACCTGTTGTCTGGAC
CCTGACCAACGTCATCCATAACTTGGCTATGTATGTCTTCTTACATACAGTAAAAGGGACACTCTTTGAGACCCCTGACC
AAGGGAAGGCTCGGCTACTGACACACTGGGAACAGATGGACTACGGGCTCCAATTTACCTCTTCCCGCAAATTCCTCAGC
ATCTCTCCTATTGTACTCTACCTCCTGGCCAGCTTCTACACCAAGTATGATGCTGCTCACTTCATCATCAACACAGCCTC
ATTGCTTAGCGTACTGCTGCCTAAGTTACCCCAATTCCATGGGGTTCGTCTCTTTGGCATCAACAAATAC

Alignment

ORF - retro_cfam_1248 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.23 %
• Parental protein coverage: 84.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAYIILVGLLHVVLLSIPFFSIPVVWTLTNVIHNLAMYVFLHTVKGTPFETPDQGKARLLTHWEQMDYGL
          LAYIILVGLLHVVLLSIPFFSIPVVWTLTNVIHNLAMYVFLHTVKGT.FETPDQGKARLLTHWEQMDYGL
Retrocopy LAYIILVGLLHVVLLSIPFFSIPVVWTLTNVIHNLAMYVFLHTVKGTLFETPDQGKARLLTHWEQMDYGL

Parental  QFTSSRKFLSISPIVLYLLASFYTKYDAAHFIINTASLLSVLLPKLPQFHGVRLFGINKY
          QFTSSRKFLSISPIVLYLLASFYTKYDAAHFIINTASLLSVLLPKLPQFHGVRLFGINKY
Retrocopy QFTSSRKFLSISPIVLYLLASFYTKYDAAHFIINTASLLSVLLPKLPQFHGVRLFGINKY

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	0.04 RPM	5.46 RPM
SRP017611_brain	0.00 RPM	3.10 RPM
SRP017611_kidney	1.12 RPM	30.77 RPM
SRP017611_liver	1.23 RPM	6.09 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1248 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1248 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1248 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000071	8 retrocopies	retro_cfam_1078, retro_cfam_1248 , retro_cfam_1512, retro_cfam_1786, retro_cfam_187, retro_cfam_335, retro_cfam_576, retro_cfam_972,
Choloepus hoffmanni	ENSCHOG00000009601	1 retrocopy	retro_chof_2232,
Erinaceus europaeus	ENSEEUG00000015224	1 retrocopy	retro_eeur_16,
Felis catus	ENSFCAG00000013964	1 retrocopy	retro_fcat_895,
Macropus eugenii	ENSMEUG00000014896	1 retrocopy	retro_meug_767,
Microcebus murinus	ENSMICG00000010920	1 retrocopy	retro_mmur_212,
Myotis lucifugus	ENSMLUG00000003575	1 retrocopy	retro_mluc_901,
Macaca mulatta	ENSMMUG00000006292	1 retrocopy	retro_mmul_2358,
Mustela putorius furo	ENSMPUG00000000911	2 retrocopies	retro_mputfur_452, retro_mputfur_738,
Mus musculus	ENSMUSG00000025353	1 retrocopy	retro_mmus_2646,
Otolemur garnettii	ENSOGAG00000001695	2 retrocopies	retro_ogar_3016, retro_ogar_951,