RetrogeneDB ID: retro_cfam_816

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 18:10058979..10059908(-)
• Located in intron of: ENSCAFG00000030906

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000008357
• Aliases: None
• Description: None

Sequence

>retro_cfam_816
ATGCTGTCTGGGTTCAATACGGCCTTCCATCCAGGTCTCGCTCTGCAGCCTCCTCCAGATCCAGCTCATGGTGGACCTTG
TGGAAATAGGGTCTTCACATCCCATCCTGGGAATCCCCAAAGTCTTTAAGAGAAACACCAACAGCAAAAAGATGAATCTG
GGAGTTGGTGCCTACCGAGATGATAATGGAAAGCCTATGTGCTCCCCAGCATCCAGAAGGCAGAAGCCCAGACTGCTGCA
AACAATATGGACAAAGAATACCTACCCATCGTGAGACTTGCTGAATTTTGTAAGGCAGCTCCAAAACTAGCCCCAGGAGA
GAACAACTAAAGGTTGAAAAGCAGCAGATATGTCACCCTGCAGACCATTTCTGCAACTAGGGCCTGAGGACTGGAGCCAA
TTTTCTGCAGAGGTTTTTTTAAGTTCAGCCGAAGTGTCTTTCTGTCCAAACCACCCTGGGGAAATCACACACCCATCTTC
AGGGATGCTGGCATGCAGCTACAAGGTTAATTGATACAATAACCCCAAGACTTGCAGCTTTGACTTTACAGGCTCTGTGG
AGGACATTTTGAAAATGCCACAACATTTTCTCCTGCTTTCCTGTCTGAGCCCACTGCCCCATGGGAGTGGACCAATGCCA
TGAGCCGTAGAAGGAAGTGGCAACAGTGATGAAAAGGAACAGTCTCTTGACGTTCTTTGACATGGCCTCCCAAGGCTTTG
CCAACAGTGATGGCAACAAAGATGCCTGGACTGTATGCCACTTCATGGAACAGGGCATTAATGTTGGTCCCTGCCAGTCC
TATGCCAAGATCATGGGCCTATCTGGTGAGCACATGGGAGCCTTCACTGTGGTCAGCAAAGATGCTGATGAAGCCAGAAG
GGTAGAGTCACAGTTGAAGATCTTGATCTGTCCCATGTATTCCAGCCCT

Alignment

ORF - retro_cfam_816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.75 %
• Parental protein coverage: 72.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  VLSGVAAAFHPGLA-GAASARASSWWTH-VEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNGKP-Y
          .LSG...AFHPGLA..AAS.R.SSWWT..VE.G...PILG....FKR.TNSKKMNLGVGAYRDDNGKP.Y
Retrocopy MLSGFNTAFHPGLA<SAASSRSSSWWTL<VEIGSSHPILGIPKVFKRNTNSKKMNLGVGAYRDDNGKP<Y

Parental  VLPSVRKAEAQIAAKNLDKEYLPIAGLAEFCKASAELALGENNEVLKSSRYVTVQTISGTGA-LRIGASF
          VLPS..KAEAQ.AA.N.DKEYLPI..LAEFCKA...LA.GENN..LKSSRYVT.QTIS.T.A.LR.GA.F
Retrocopy VLPSIQKAEAQTAANNMDKEYLPIVRLAEFCKAAPKLAPGENN*RLKSSRYVTLQTISATRA<LRTGANF

Parental  LQRFF-KFSQDVFLPKPSWGNHTPIFRDAGMQLHGYRYYDP-KTCGFDFTGAIEDISKMPQQSVLLLHAC
          LQRFF.KFS..VFL.KP.WGNHTPIFRDAGMQL.G.....P.KTC.FDFTG..EDI.KMPQ...LLL...
Retrocopy LQRFF>KFSRSVFLSKPPWGNHTPIFRDAGMQLQG*LIQ*P>KTCSFDFTGSVEDILKMPQH-FLLLSCL

Parental  AHNPTGVDPRP-EQWKEIATVVKKNNLFAFFDMAYQGFASGDGNKDAWAVRHFIEQGINVCLCQSYAKNM
          ...P.G..P.P.E..KE.ATV.K.N.L..FFDMA.QGFA..DGNKDAW.V.HF.EQGINV..CQSYAK.M
Retrocopy SPLPHGSGPMP>EP*KEVATVMKRNSLLTFFDMASQGFANSDGNKDAWTVCHFMEQGINVGPCQSYAKIM

Parental  GLYGERVGAFTVVCKDADEAKRVESQLKILIRPMYSNP
          GL.GE..GAFTVV.KDADEA.RVESQLKILI.PMYS.P
Retrocopy GLSGEHMGAFTVVSKDADEARRVESQLKILICPMYSSP

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	42.25 RPM
SRP017611_brain	0.00 RPM	45.81 RPM
SRP017611_kidney	0.00 RPM	69.87 RPM
SRP017611_liver	0.00 RPM	54.68 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_816 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_816 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_816 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017346	3 retrocopies	retro_amel_1805, retro_amel_815, retro_amel_846,
Canis familiaris	ENSCAFG00000008357	2 retrocopies	retro_cfam_586, retro_cfam_816 ,
Callithrix jacchus	ENSCJAG00000011234	1 retrocopy	retro_cjac_2916,
Equus caballus	ENSECAG00000016504	1 retrocopy	retro_ecab_694,
Felis catus	ENSFCAG00000025552	3 retrocopies	retro_fcat_1068, retro_fcat_1888, retro_fcat_381,
Homo sapiens	ENSG00000125166	4 retrocopies	retro_hsap_4687, retro_hsap_473, retro_hsap_960, retro_hsap_971,
Gorilla gorilla	ENSGGOG00000005767	3 retrocopies	retro_ggor_2912, retro_ggor_449, retro_ggor_774,
Macropus eugenii	ENSMEUG00000012574	1 retrocopy	retro_meug_2109,
Microcebus murinus	ENSMICG00000008954	1 retrocopy	retro_mmur_480,
Macaca mulatta	ENSMMUG00000006000	1 retrocopy	retro_mmul_1337,
Mustela putorius furo	ENSMPUG00000004862	1 retrocopy	retro_mputfur_567,
Mus musculus	ENSMUSG00000031672	1 retrocopy	retro_mmus_2701,
Oryctolagus cuniculus	ENSOCUG00000003871	1 retrocopy	retro_ocun_1516,
Otolemur garnettii	ENSOGAG00000000551	2 retrocopies	retro_ogar_2182, retro_ogar_827,
Pongo abelii	ENSPPYG00000007413	3 retrocopies	retro_pabe_3640, retro_pabe_823, retro_pabe_901,
Pan troglodytes	ENSPTRG00000008185	4 retrocopies	retro_ptro_3115, retro_ptro_354, retro_ptro_665, retro_ptro_670,
Rattus norvegicus	ENSRNOG00000011782	1 retrocopy	retro_rnor_2695,
Tupaia belangeri	ENSTBEG00000001808	1 retrocopy	retro_tbel_3799,