RetrogeneDB ID: retro_cfam_1654

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:36278973..36279222(+)
• Located in intron of: ENSCAFG00000016541

Retrocopy information

• Ensembl ID: ENSCAFG00000016545
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: cfa-mir-147
• Ensembl ID: ENSCAFG00000031501
• Aliases: None
• Description: cfa-mir-147 [Source:miRBase;Acc:MI0010371]

Sequence

>retro_cfam_1654
ATTAACTTTTTCCAACTCCTGATGAAAAAGAAGGAACTTATTCCTTTGGTGCTGTTCATGGCCACAGCGGCAGGCGGAGC
TTCGTCTTTCGATGTATATTCCCTTCAAAAATCTGATGTGATCCTAGATCGGAAAAGAAATCCAGAACCTTGGGAAACCA
TGGACCCTAGTGTACCTAGCAAGCTTATAACAATCAACCAAGAATGGAAGCCCATTGAAGAGTTGCGGAAGGTCCGAAGA
GCCACTAAA

Alignment

ORF - retro_cfam_1654 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.18 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNFFQLLMKKKELIPLVLFMATAAGGASSFAVYSLQKSDVILDRKRNPEPWETVDPSVPSKLITINQEWK
          .NFFQLLMKKKELIPLVLFMATAAGGASSF.VYSLQKSDVILDRKRNPEPWET.DPSVPSKLITINQEWK
Retrocopy INFFQLLMKKKELIPLVLFMATAAGGASSFDVYSLQKSDVILDRKRNPEPWETMDPSVPSKLITINQEWK

Parental  PIEELQKVRRATK
          PIEEL.KVRRATK
Retrocopy PIEELRKVRRATK

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	0.34 RPM	0.17 RPM
SRP017611_brain	0.24 RPM	0.16 RPM
SRP017611_kidney	0.00 RPM	10.63 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1654 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1654 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1654 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031501	2 retrocopies	retro_cfam_1654 , retro_cfam_669,
Cavia porcellus	ENSCPOG00000020706	1 retrocopy	retro_cpor_450,
Erinaceus europaeus	ENSEEUG00000003556	1 retrocopy	retro_eeur_594,
Macropus eugenii	ENSMEUG00000013137	4 retrocopies	retro_meug_1593, retro_meug_2033, retro_meug_278, retro_meug_63,
Monodelphis domestica	ENSMODG00000028279	1 retrocopy	retro_mdom_225,
Oryctolagus cuniculus	ENSOCUG00000029216	1 retrocopy	retro_ocun_33,
Rattus norvegicus	ENSRNOG00000050251	1 retrocopy	retro_rnor_484,
Sarcophilus harrisii	ENSSHAG00000006433	3 retrocopies	retro_shar_296, retro_shar_416, retro_shar_744,
Ictidomys tridecemlineatus	ENSSTOG00000021929	1 retrocopy	retro_itri_1133,