RetrogeneDB ID: retro_cfam_136

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:1851976..1852570(-)
• Located in intron of: ENSCAFG00000003705

Retrocopy information

• Ensembl ID: ENSCAFG00000029571
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000004823
• Aliases: None
• Description: None

Sequence

>retro_cfam_136
ACTCATCAGTCAAAAATCAAGTATGACTGGTATCAAACAGAATCTCAAGTAATCATTACACTTATGATCAAGAATGTTCA
GAAGAATAATGTAAATGTGGAATTTTCAGAAAAAGAGTTGTCTGCTTTGGTGAAACTTCCTTCTGGAGAGGATTACAATT
TGAAACTGAGACTTCTTCATCCTATAATACCAGAACAGAGCACATTTAAAGTACTTTCGACAAAGATTGAAATTAAAATG
AAAAAGACAGAGGCTGTGAGATGGGAAAAGCTAGAGGGGCAAGGAGATGTGCCTAAACCAAAACAGTTCATAGCAGATGT
AAAGAACTTATATCCATCGTCATCTCATTATACAAGAAATTGGGATAAATTGGTTGGTGAGATCAAAGAAGAAGAAAAAA
ATGAGAAGTTGGAGGTAGATGCAGCTTTAAACAAATTATTTCAGCAGATCTATTCAGATGGTTCTGATGAAGTGAAACGT
GCCATGAACAAATCATTTATGGAGTCTGGTGGTACAGTTTTGAGTACCAACTGGTCTGATGTAGGTAAAAGGAAAGTTGA
AATCAACCCTCCTGATGATATGGACTGGAAAAAG

Alignment

ORF - retro_cfam_136 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  THQSKIKYDWYQTESQVIITLMIKNVQKNNVNVEFSEKELSALVKLPSGEDYNLKLRLLHPIIPEQSTFK
          THQSKIKYDWYQTESQVIITLMIKNVQKNNVNVEFSEKELSALVKLPSGEDYNLKLRLLHPIIPEQSTFK
Retrocopy THQSKIKYDWYQTESQVIITLMIKNVQKNNVNVEFSEKELSALVKLPSGEDYNLKLRLLHPIIPEQSTFK

Parental  VLSTKIEIKMKKTEAVRWEKLEGQGDVPKPKQFIADVKNLYPSSSHYTRNWDKLVGEIKEEEKNEKLEGD
          VLSTKIEIKMKKTEAVRWEKLEGQGDVPKPKQFIADVKNLYPSSSHYTRNWDKLVGEIKEEEKNEKLE.D
Retrocopy VLSTKIEIKMKKTEAVRWEKLEGQGDVPKPKQFIADVKNLYPSSSHYTRNWDKLVGEIKEEEKNEKLEVD

Parental  AALNKLFQQIYSDGSDEVKRAMNKSFMESGGTVLSTNWSDVGKRKVEINPPDDMEWKK
          AALNKLFQQIYSDGSDEVKRAMNKSFMESGGTVLSTNWSDVGKRKVEINPPDDM.WKK
Retrocopy AALNKLFQQIYSDGSDEVKRAMNKSFMESGGTVLSTNWSDVGKRKVEINPPDDMDWKK

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	0.59 RPM	6.68 RPM
SRP017611_brain	1.27 RPM	4.45 RPM
SRP017611_kidney	1.12 RPM	9.51 RPM
SRP017611_liver	0.22 RPM	2.61 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_136 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_136 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008606	2 retrocopies	retro_amel_353, retro_amel_896,
Canis familiaris	ENSCAFG00000004823	1 retrocopy	retro_cfam_136 ,
Callithrix jacchus	ENSCJAG00000003604	1 retrocopy	retro_cjac_310,
Cavia porcellus	ENSCPOG00000003374	1 retrocopy	retro_cpor_110,
Dasypus novemcinctus	ENSDNOG00000002991	1 retrocopy	retro_dnov_2621,
Homo sapiens	ENSG00000165416	1 retrocopy	retro_hsap_2628,
Gorilla gorilla	ENSGGOG00000006797	1 retrocopy	retro_ggor_1840,
Nomascus leucogenys	ENSNLEG00000015700	1 retrocopy	retro_nleu_640,
Otolemur garnettii	ENSOGAG00000008220	1 retrocopy	retro_ogar_41,
Pan troglodytes	ENSPTRG00000005906	1 retrocopy	retro_ptro_1773,