RetrogeneDB ID: retro_cfam_580

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:49637299..49638115(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000008716
• Aliases: None
• Description: None

Sequence

>retro_cfam_580
CACCACCCCTTTCACCTCTTGGTAGTTGGAAATTAAGCTGTTATCATTTCTGGAAGGAAACTTGCCAGCAGATCAAGCAG
GAAGTGCAGTAGGAGGTGGAAGAATGGGTGACATTGGGCAACAAAGTGGCCACACCTGAGCATGGTTCTGGTTGGTGAGA
ATCCTGCAAGTCACTCCTAGGACCTCAACAAAACCAAGGTACCTACAGAGGTGGGAATAAAAAATGAGACAATTGTGAAA
CCAGTGTCAATTTCAGAGGAAGAACTGTTGAATTTAATCAATAATCTAAATAATGATAATGTAGATGGCCTCCTTGTTCA
GCTGCCTCTTCCAGAGCACACTGAGGAGAGAAAGATCTGCAATGCTGTTTCTCCAGACAAGGTTATTGATGGCTTTCATA
TAATTAATATAGGAGGAATGTGTTTGGATCAGTATTCCATGTTATTGGCTACCCCATGCAATGTCTGGGAAATAATTAAA
TGAACTAGCATCCCAACTCTAGGGAAGAACATGATTGTGGCTGGAGGTCAAATGTTGGAATGCCCATTGCAATTCTATCA
CACACAGATGGAGTGCATGGATATCCTGGAGGCAATGCCATTGTTCTATATCTCATCAATACACTCCCAAAGAACTGAAG
AAACATACAATTCTTACAGACATTATGGTCTCTGTTGCAGACAGTCCAAATATGATCACAGAAGATATGATCAAGGAGGG
AGCAGTAGTCACCCATGTGGGAATAAATAGAGTTCAAGATCCCCTAATGGCTAAATCCAATCAGTTGGAAATGTGGATTT
TGAGTCAGAAGGAAAA

Alignment

ORF - retro_cfam_580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.31 %
• Parental protein coverage: 78.86 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  HRPFHLSVVRDEAVIISGRKLA-QQIKQEVRQEVEEWVASGNKR-PHLSVVLVGENPASHSYVLNKTRAA
          H.PFHL.VV...AVIISGRKLA.QQIKQEV..EVEEWV..GNK..PHLS.VLVGENPASHS..LNKT...
Retrocopy HHPFHLLVVGN*AVIISGRKLA<QQIKQEVQ*EVEEWVTLGNKV>PHLSMVLVGENPASHS*DLNKTKVP

Parental  AEVGINSETIVKPASISEDELLNLINKLNNDDNVDGLLVQLPLPEHIDERKVCNAVSPDKDVDGFHVINV
          .EVGI..ETIVKP.SISE.ELLNLIN.LNN.DNVDGLLVQLPLPEH..ERK.CNAVSPDK..DGFH.IN.
Retrocopy TEVGIKNETIVKPVSISEEELLNLINNLNN-DNVDGLLVQLPLPEHTEERKICNAVSPDKVIDGFHIINI

Parental  GRMCLDQYSMLPATPWGVWEIIKRTGIPTLGKNVVVAG-RSKNVGMPIAMLLHTDGAHERPGGDATV-TI
          G.MCLDQYSML.ATP..VWEIIK.T.IPTLGKN..VAG.RS.NVGMPIA.L.HTDG.H..PGG.A.V..I
Retrocopy GGMCLDQYSMLLATPCNVWEIIK*TSIPTLGKNMIVAG<RS-NVGMPIAILSHTDGVHGYPGGNAIV<SI

Parental  SHRYTPKEQLKKHTVLADIVISAAGIPNLITADMIKEGAAVIDVGINRVQDPITAKP-KLVGDVDFEGVR
          SH.YTPKE.LKKHT.L.DI..S.A..PN.IT.DMIKEGA.V..VGINRVQDP..AK....VG.VDFE...
Retrocopy SHQYTPKE-LKKHTILTDIMVSVADSPNMITEDMIKEGAVVTHVGINRVQDPLMAKS<QSVGNVDFESEG

Parental  K
          K
Retrocopy K

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	19.95 RPM
SRP017611_brain	0.00 RPM	3.10 RPM
SRP017611_kidney	0.00 RPM	0.79 RPM
SRP017611_liver	0.00 RPM	0.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_580 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_580 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_580 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017345	2 retrocopies	retro_amel_1098, retro_amel_1584,
Canis familiaris	ENSCAFG00000008716	1 retrocopy	retro_cfam_580 ,
Callithrix jacchus	ENSCJAG00000017810	3 retrocopies	retro_cjac_2225, retro_cjac_2568, retro_cjac_3078,
Homo sapiens	ENSG00000065911	5 retrocopies	retro_hsap_2732, retro_hsap_2817, retro_hsap_3002, retro_hsap_3309, retro_hsap_3874,
Macropus eugenii	ENSMEUG00000013987	4 retrocopies	retro_meug_1468, retro_meug_152, retro_meug_1577, retro_meug_2074,
Mustela putorius furo	ENSMPUG00000007829	3 retrocopies	retro_mputfur_1087, retro_mputfur_1397, retro_mputfur_1551,
Nomascus leucogenys	ENSNLEG00000000326	5 retrocopies	retro_nleu_1196, retro_nleu_207, retro_nleu_2501, retro_nleu_595, retro_nleu_749,
Otolemur garnettii	ENSOGAG00000009089	1 retrocopy	retro_ogar_3390,
Pongo abelii	ENSPPYG00000012283	3 retrocopies	retro_pabe_2271, retro_pabe_2729, retro_pabe_3077,
Pan troglodytes	ENSPTRG00000012081	4 retrocopies	retro_ptro_1846, retro_ptro_1910, retro_ptro_2162, retro_ptro_2641,
Pteropus vampyrus	ENSPVAG00000013948	2 retrocopies	retro_pvam_1357, retro_pvam_1414,
Rattus norvegicus	ENSRNOG00000010833	1 retrocopy	retro_rnor_2170,