RetrogeneDB ID: retro_cfam_461

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:35522710..35523374(-)
• Located in intron of: ENSCAFG00000001545

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000006693
• Aliases: None
• Description: Small nuclear ribonucleoprotein-associated protein [Source:UniProtKB/TrEMBL;Acc:E2R1C4]

Sequence

>retro_cfam_461
ATGACTACGGGCAATAACAGCAAGATGCTGCAGCACATCGACTACAGGATGGAGGTGCATCCTACAAGACGGCCGGATCT
TCATTGGCACCTTCAAGGCTTTTGACAATGATATAAATTTGGTCCTCTGTGACTGTGATAGGTTCAGGAAGATCAAGCCA
AAGAACTCAAAACAAGCAGAAAGAAAAGAGAAGTGAGTCCTCGGTCTGGTGCTGCTTTGTGGGGAGAACCTGGTCTCAGT
GACAGTAGATGGACCTCCTCCCAAAGATACTGGCATTGCCTGAGTGCCACTTGCTGGAGCTGCCGGGAGCCCAGGGATTG
GCAGGGCTGCTGGTAGAGGAATTCCAGCTGGTGTTCCAATGCCCTAGACTCCTGCCGGGCTTGCAGGGCCTGTCTGAGGA
GTTGGTGGGCCATTCCAGCAGGTGATGACCCCACAGGGAGGAGGCACTGTGGCTGTCGCTGTAGCTGCTGCCACTGCCAG
CATTGCTGGGGCTCCGGCCCAGTACCTGTTCGGCCGTGGGGGTCCTCCCCACCTACTGGCCAAGGGACACCCCCTCCAGG
CACGATGGGCCCACCACCTGGCATGAGGCTTCCCATGGGGACCCCCGATGGGGATCCCTCCTGGATGAGGAACTCTGATG
GGCATGCCCCTCCTGGGGATGCAG

Alignment

ORF - retro_cfam_461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.04 %
• Parental protein coverage: 95.67 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTVGKSSKMLQHIDYRM-RCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGL
          MT.G..SKMLQHIDYRM.RCILQDGRIFIGTFKAFD...NL.LCDCD.FRKIKPKNSKQAER.EK.VLGL
Retrocopy MTTGNNSKMLQHIDYRM>RCILQDGRIFIGTFKAFDNDINLVLCDCDRFRKIKPKNSKQAERKEK*VLGL

Parental  VLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQ
          VLL.GENLVS.TV.GPPPKDTGIA.VPLAGAAG.PGIGRAAGRGIPAGVPMP..PAGLAGPV.GVGGP.Q
Retrocopy VLLCGENLVSVTVDGPPPKDTGIA*VPLAGAAGSPGIGRAAGRGIPAGVPMP*TPAGLAGPV*GVGGPFQ

Parental  QVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPP-PPMGRGAPPPGMMGPPPGMRPPM-GPPMGIPP
          QVMTPQG.GTVA.A.AAATASIAGAP.QY..GRGGPP.PP.G.G.PPPG.MGPPPGMR.PM.GPPMGIPP
Retrocopy QVMTPQGGGTVAVAVAAATASIAGAPAQYLFGRGGPP<PPTGQGTPPPGTMGPPPGMRLPM>GPPMGIPP

Parental  GRGTPMGMPPPGMR
          G.GT.MGMP..GM.
Retrocopy G*GTLMGMPLLGMQ

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	82.02 RPM
SRP017611_brain	0.24 RPM	22.55 RPM
SRP017611_kidney	0.00 RPM	72.64 RPM
SRP017611_liver	0.00 RPM	21.03 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_461 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_461 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_461 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011353	1 retrocopy	retro_amel_1403,
Canis familiaris	ENSCAFG00000006693	3 retrocopies	retro_cfam_1268, retro_cfam_1773, retro_cfam_461 ,
Canis familiaris	ENSCAFG00000010127	6 retrocopies	retro_cfam_1753, retro_cfam_1874, retro_cfam_2039, retro_cfam_627, retro_cfam_682, retro_cfam_752,
Callithrix jacchus	ENSCJAG00000020971	2 retrocopies	retro_cjac_172, retro_cjac_1739,
Dasypus novemcinctus	ENSDNOG00000007896	2 retrocopies	retro_dnov_2060, retro_dnov_2471,
Erinaceus europaeus	ENSEEUG00000015568	3 retrocopies	retro_eeur_312, retro_eeur_434, retro_eeur_6,
Felis catus	ENSFCAG00000014447	2 retrocopies	retro_fcat_1788, retro_fcat_1960,
Microcebus murinus	ENSMICG00000016519	4 retrocopies	retro_mmur_1012, retro_mmur_1478, retro_mmur_546, retro_mmur_861,
Myotis lucifugus	ENSMLUG00000016951	1 retrocopy	retro_mluc_1725,
Mustela putorius furo	ENSMPUG00000009283	1 retrocopy	retro_mputfur_1153,
Mus musculus	ENSMUSG00000027404	3 retrocopies	retro_mmus_2938, retro_mmus_3450, retro_mmus_554,
Nomascus leucogenys	ENSNLEG00000009206	1 retrocopy	retro_nleu_761,
Otolemur garnettii	ENSOGAG00000016149	4 retrocopies	retro_ogar_2197, retro_ogar_2841, retro_ogar_2918, retro_ogar_3236,
Ochotona princeps	ENSOPRG00000007459	2 retrocopies	retro_opri_697, retro_opri_72,
Pongo abelii	ENSPPYG00000010841	1 retrocopy	retro_pabe_2265,
Pteropus vampyrus	ENSPVAG00000017013	1 retrocopy	retro_pvam_289,
Rattus norvegicus	ENSRNOG00000006961	2 retrocopies	retro_rnor_2825, retro_rnor_474,
Tupaia belangeri	ENSTBEG00000010040	3 retrocopies	retro_tbel_1117, retro_tbel_1171, retro_tbel_2839,
Tarsius syrichta	ENSTSYG00000014498	2 retrocopies	retro_tsyr_45, retro_tsyr_719,