RetrogeneDB ID: retro_cfam_112

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 17:11673452..11674349(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000003714
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000007112
• Aliases: None
• Description: None

Sequence

>retro_cfam_112
ATGTCTCTCTACCCATCTCTTGAAGACCTGAAGGTAGACAAAGTTCTTCAGGCTCAAACTGCCTTTTCTGCAAACCCTGC
CAACCCAGCAATTTTGTCTGAAGCTTCTGCTCCCATCTCTCAAGATGGAAATCTCTATCCTAAACTATATCTGGAGCTGT
CCCAGTACATGGGCCTGAGTTTAAATGATGAAGAAATCCGTGCAAATATGGCCTTGGCCCCTGGAGCATCAGTTCAGGGG
CAGTTGGTAGCAAGACCTTCCAGTATGAACTATATGGTAGCTCCTGTAACTGGTAACGATGTTGGAATTCGTAGAGCAGA
AATTAAGCAAGGGATTCGCGAAGTCATTTTGTGCAAGGATCAAGATGGAAAAATTAGACTCAGGCTTAAATCAATAGATA
ATGGTATATTTGTTCAGCTGGTCCAGGCAAATTCTCCAGCCTCGTTGGTTGGTCTGAGATTTGGGGACCAAGTACTCCAG
ATCAATGGGGAAAACTGTGCAGGCTGGAGCTCTGATAAAGCTCACAAGGTGCTCAAACAGGCTTTTGGAGAGAAGACTAC
TATGACTGTTCGTGACAGGCCCTTTGAACGGACAGTTACCATGCGTAAGGATAGTACTGGACATGTTGGTTTTATCTTTA
AAAATGGAAAGATAACATCCATAGTGAAAGATAGTTCTGCAGCCAGAAATGGTCTTCTCACAGAACTTAACACCTGTGAA
GTCAATGGGCAGAATGTCATTGGGCTGAAGGACTCTCAAATTGCAGACATACTGTCAACATCTGAGACTGTAGTTACTAT
TACAATCAGGCCTGCTTTTATCTTTGAACATATTATTAAACGGATGGCACCAAGCATTATGAAGAGCCTGATGGATCACA
CCATTCCTGAGGTTTAA

Alignment

ORF - retro_cfam_112 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLYPSLEDLKVDKVLQAQTAFSANPANPAILSEASAPISQDGNLYPKLYPELSQYMGLSLNDEEIRANM
          MSLYPSLEDLKVDKVLQAQTAFSANPANPAILSEASAPISQDGNLYPKLY.ELSQYMGLSLNDEEIRANM
Retrocopy MSLYPSLEDLKVDKVLQAQTAFSANPANPAILSEASAPISQDGNLYPKLYLELSQYMGLSLNDEEIRANM

Parental  ALAPGASVQG-LVARPSSMNYMVAPVTGNDVGIRRAEIKQGIREVILCKDQDGKIGLRLKSIDNGIFVQL
          ALAPGASVQG.LVARPSSMNYMVAPVTGNDVGIRRAEIKQGIREVILCKDQDGKI.LRLKSIDNGIFVQL
Retrocopy ALAPGASVQGQLVARPSSMNYMVAPVTGNDVGIRRAEIKQGIREVILCKDQDGKIRLRLKSIDNGIFVQL

Parental  VQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTVRDRPFERTVTMHKDSTGHVG
          VQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEK.TMTVRDRPFERTVTM.KDSTGHVG
Retrocopy VQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKTTMTVRDRPFERTVTMRKDSTGHVG

Parental  FIFKNGKITSIVKDSSAARNGLLTEHNICEVNGQNVIGLKDSQIADILSTSETVVTITIMPAFIFEHIIK
          FIFKNGKITSIVKDSSAARNGLLTE.N.CEVNGQNVIGLKDSQIADILSTSETVVTITI.PAFIFEHIIK
Retrocopy FIFKNGKITSIVKDSSAARNGLLTELNTCEVNGQNVIGLKDSQIADILSTSETVVTITIRPAFIFEHIIK

Parental  RMAPSIMKSLMDHTIPEV
          RMAPSIMKSLMDHTIPEV
Retrocopy RMAPSIMKSLMDHTIPEV

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	1.26 RPM	40.99 RPM
SRP017611_brain	2.54 RPM	43.75 RPM
SRP017611_kidney	5.22 RPM	80.70 RPM
SRP017611_liver	1.31 RPM	25.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_112 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_112 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006161	1 retrocopy	retro_amel_654,
Bos taurus	ENSBTAG00000019910	2 retrocopies	retro_btau_1035, retro_btau_383,
Canis familiaris	ENSCAFG00000007112	1 retrocopy	retro_cfam_112 ,
Choloepus hoffmanni	ENSCHOG00000003565	5 retrocopies	retro_chof_1063, retro_chof_1151, retro_chof_1910, retro_chof_713, retro_chof_970,
Equus caballus	ENSECAG00000015053	1 retrocopy	retro_ecab_439,
Homo sapiens	ENSG00000137575	2 retrocopies	retro_hsap_3971, retro_hsap_4810,
Gorilla gorilla	ENSGGOG00000009019	2 retrocopies	retro_ggor_2666, retro_ggor_2995,
Loxodonta africana	ENSLAFG00000010757	1 retrocopy	retro_lafr_1044,
Microcebus murinus	ENSMICG00000003968	1 retrocopy	retro_mmur_170,
Myotis lucifugus	ENSMLUG00000004807	1 retrocopy	retro_mluc_12,
Macaca mulatta	ENSMMUG00000017296	1 retrocopy	retro_mmul_2564,
Mustela putorius furo	ENSMPUG00000010339	5 retrocopies	retro_mputfur_1055, retro_mputfur_1340, retro_mputfur_292, retro_mputfur_829, retro_mputfur_933,
Nomascus leucogenys	ENSNLEG00000001408	2 retrocopies	retro_nleu_2185, retro_nleu_2525,
Otolemur garnettii	ENSOGAG00000013462	1 retrocopy	retro_ogar_3259,
Procavia capensis	ENSPCAG00000016432	1 retrocopy	retro_pcap_186,
Pongo abelii	ENSPPYG00000018612	3 retrocopies	retro_pabe_3265, retro_pabe_3266, retro_pabe_3738,
Pan troglodytes	ENSPTRG00000020277	2 retrocopies	retro_ptro_2696, retro_ptro_3200,
Tupaia belangeri	ENSTBEG00000013965	1 retrocopy	retro_tbel_2142,