RetrogeneDB ID: retro_cfam_160

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:53557778..53558345(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000008479
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000030220
• Aliases: None
• Description: None

Sequence

>retro_cfam_160
TGCTGTCAGGGGTCCCATCCGCATGGGGTGAAGCGTTCAGCCTCCCCAGACGACGATCTTGGATCTAGCAATTGGGAAGC
AGCAGACTTAGGTAATGAAGAAAGAAAACAGAAGTTCTTGAGATTTATGGGTGCAGGAAAGAAAGAACATACTGGCAGTC
TTGTTATAAGAGACCACAAATCAACATCTCACTTCCGAACAGGGGAAGAAGACAAGAAAATTAATGAAGAACTGGAGTCT
CAATATCAGCAAAGTATGGACAGTAAATTATCAAGAAGATATCGACGACATTGTGGACTTGGCTTCGGCGAGGTAGAAGA
TCATGATGGAGAAGGTGATGTGGCTGGAGATGATGATGATGATGATGATGATGATGATGATGATGATGATGATTCACCTG
ATCCTGAAAGTCCAGATGACTCTGAAAGTGATTCAGAGTCAGAGAAAGAAGAGTCTGCTGAAGGACTCCAAGCTACTGAG
CACCCTGATGAAGTAGAGGATCCCAAAGACAAAAAAGATGCAAAAAGCAACTATAAAATGATGTTTGTTAAATCCAGTGG
TTCATAA

Alignment

ORF - retro_cfam_160 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.96 %
• Parental protein coverage: 96.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SHPHGVKRSASPDDDLGSSNWEAADLGNEERKQKFLRLMGAGKKEHTGRLVIGDHKSTSHFRTGEEDKKI
          SHPHGVKRSASPDDDLGSSNWEAADLGNEERKQKFLR.MGAGKKEHTG.LVI.DHKSTSHFRTGEEDKKI
Retrocopy SHPHGVKRSASPDDDLGSSNWEAADLGNEERKQKFLRFMGAGKKEHTGSLVIRDHKSTSHFRTGEEDKKI

Parental  NEELESQYQQSMDSKLSGRYRRHCGLGFSEVEDHDGEGDVAGDDDDDDDSPD---PESPD-DSESDSESE
          NEELESQYQQSMDSKLS.RYRRHCGLGF.EVEDHDGEGDVAGDDDDDDD..D.....SPD..S..DSES.
Retrocopy NEELESQYQQSMDSKLSRRYRRHCGLGFGEVEDHDGEGDVAGDDDDDDDDDDDDDDDSPDPESPDDSESD

Parental  KE----ESAEELQATEHPDEVEDPKNKKDAKSNYKMMFVKSSGS
          .E....ESAE.LQATEHPDEVEDPK.KKDAKSNYKMMFVKSSGS
Retrocopy SESEKEESAEGLQATEHPDEVEDPKDKKDAKSNYKMMFVKSSGS

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	76.94 RPM
SRP017611_brain	0.24 RPM	38.51 RPM
SRP017611_kidney	0.40 RPM	93.64 RPM
SRP017611_liver	0.00 RPM	24.51 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_160 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_160 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_160 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030220	2 retrocopies	retro_cfam_160 , retro_cfam_717,
Callithrix jacchus	ENSCJAG00000009626	1 retrocopy	retro_cjac_3098,
Cavia porcellus	ENSCPOG00000009679	2 retrocopies	retro_cpor_1331, retro_cpor_772,
Equus caballus	ENSECAG00000011778	1 retrocopy	retro_ecab_269,
Felis catus	ENSFCAG00000027747	1 retrocopy	retro_fcat_2016,
Homo sapiens	ENSG00000110696	2 retrocopies	retro_hsap_1408, retro_hsap_3898,
Macropus eugenii	ENSMEUG00000011795	1 retrocopy	retro_meug_1432,
Myotis lucifugus	ENSMLUG00000001589	1 retrocopy	retro_mluc_2604,
Monodelphis domestica	ENSMODG00000007147	2 retrocopies	retro_mdom_1249, retro_mdom_672,
Mus musculus	ENSMUSG00000030663	2 retrocopies	retro_mmus_2190, retro_mmus_2616,
Nomascus leucogenys	ENSNLEG00000017719	1 retrocopy	retro_nleu_1425,
Otolemur garnettii	ENSOGAG00000025335	2 retrocopies	retro_ogar_1613, retro_ogar_2569,
Ochotona princeps	ENSOPRG00000000154	1 retrocopy	retro_opri_761,
Pongo abelii	ENSPPYG00000003458	2 retrocopies	retro_pabe_1166, retro_pabe_3178,
Rattus norvegicus	ENSRNOG00000020436	1 retrocopy	retro_rnor_622,