RetrogeneDB ID: retro_cfam_1047

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:19349561..19350885(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOLC1
• Ensembl ID: ENSCAFG00000010062
• Aliases: None
• Description: nucleolar and coiled-body phosphoprotein 1 [Source:HGNC Symbol;Acc:15608]

Sequence

>retro_cfam_1047
ATACCTAAGAAGACTGTACCTAAAAAGCAAGTTGTAGTCAAGTCCCCAGTGAAAGCAGGGGCCACCACTACCCAAAAGAG
TTCCAGCAGTGAGGAGGAGGAGAAGGAAGAGCAGAAAAAAAACATGAAGAAAAAACCAGGTCCCTATAGTTCAGTCCTCC
CGCCTTCTGCTGCCTCCTCAGAAAGTCTCCCAAGAAAGCCACAGAGAAGAAACAGCCTGTGGAGAGCAGTGAGGACAGCA
GTGATGAGTCTGATTCAAGTTCAGAGGAAGAAAAGAAACCCCCAGCTAAGGCAGTCATCTCTAAAGCAACCACTAAACCA
GCTCCAGCAAAGAAAGAACCAGAGAACTCTTCAGACAGCTGAGACTCTGACAGTTCTGAGGATGAAGCTCCTGCCAAGCC
AACCAGTACCGCCAAGAATCTATCAAGTAGGCCACTTACCACTCCCAGGCAACCTGCGGCTAAACCAGCCACAGCTCCCA
AGCAACCTGCAGGTAGTGGCCAGAAGCCATTGACCAGAAAGGCTGATAGCAGCTCCAGTGAAGAGGAGAAAACAAAGAAG
ACCCTGGTCACCCCCAAGCCCAAGGCAGTGGCTAAGGCAGCTCCTTCTTTGCCTATCAAACAGGCTTCCTAGGGTGATGG
AAGCTCTGATTCAGATAGCTCTAGCAGTGAGGAAGAGAAGATGTCAAAATCCCCAGTTAAAAAGAAGCCACAGAAGGTGG
CAAGAGTTGTAGCCTCTTCCAAGGCTGCTTCCACAAAGAAAGCAAAGGCTGAGAGCAGCAGCAGTTCTTCCTCTGATGAC
TCCATTGAGGAAGAGGAAAAGGAGAAGCCTAAGGGCAAGGGCACTGTAAGGCTACAAGCCCTCAAGACCAATGGGACTCT
GCACTGAATACCCAGAAGGGAAAAGCAGATGGAGATAGCAGTGAGGAAGAAGAAGAGAAAAAGGCAGTAGTGGCAGTTTC
TAAGCCAGGTTCAGGGAAGAAGGGGAAGCAGAATGAGGCTGCCAAGGAGGCAGAGACTCCTCAAGCCAAGAGGATAAAGC
CCCAGACCCCTAACACATTTCCAAGAAGGAAGAAAGGAGAGAAAAGGGCATCACCCCCATTCCAAAGGATCAGGGAGGAG
GAAATTGAGGTAGATGCTCGAGTGGCAGACAATTCCTTCAATGCCAAGTGGGGTACAGCTGGAGACTGGGGGGAGCACGC
CAATCAGGTTCTGAAGTTCACCAAAGGCAAATCATTCCAGTATGAGAAAACCAAGAAGAAGCGGGGCAGCTCTCGGGGAG
GCTCCATTTCCATCCAGGTCAATTCCATTAAGTTTGACAGCGAG

Alignment

ORF - retro_cfam_1047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.74 %
• Parental protein coverage: 64.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LPKKQVVAKSPVKAAATTTQKSSSSEDSSSEEEEEEEEQKKPMKKKPGPYSSVPPPSVAPSKKS-LGTQA
          .PKK.V..K..V...............SSS...EEEE...........P....P..SV.P.....L....
Retrocopy IPKKTVPKKQVVVKSPVKAGATTTQKSSSS---EEEEKEEQXXXXXXXPG---PYSSVLPPSAA<LLRKS

Parental  PKKATEKKQPVESSEDSSDESDSSSEEEKKPPAKAVISKATIKPAPAKKEPESSSDSSDSDSSEDEAPAK
          PKKATEKKQPVESSEDSSDESDSSSEEEKKPPAKAVISKAT.KPAPAKKEPE.SSDS.DSDSSEDEAPAK
Retrocopy PKKATEKKQPVESSEDSSDESDSSSEEEKKPPAKAVISKATTKPAPAKKEPENSSDS*DSDSSEDEAPAK

Parental  PAGTTKNLSCRPVTTPKQPAAKPVTAPKQPAGSGQKPLTRKADSSSSEEESSSSEEEKTKKTVVTPKPKA
          P..T.KNLS.RP.TTP.QPAAKP.TAPKQPAGSGQKPLTRKADSSSSEEE.......KT..T........
Retrocopy PTSTAKNLSSRPLTTPRQPAAKPATAPKQPAGSGQKPLTRKADSSSSEEEKT----KKTLVTPKPKAVAK

Parental  VAKAVPSLPTKQASQGDGDSSSDSDSSSSEEEKMSKSPVKKKPQKVARVVASSKAASTKKAKAESSSSSS
          .A...P..............SS.S...........K.P.K..........AS.K.A...KA...S..SSS
Retrocopy AAPSLPIKQAS*GDGSSDSDSSSSEEEKMSKSPVKKKPQKVARVVASSKAASTKKA---KAESSS--SSS

Parental  SDDSSEEEEKEKPKGKGTVRPQALKTNGT-SALTTQNGKADRDSNEEEEEKKKAVVAVSKPGSGKKRKQN
          SDDS.EEEEKEKPKGKGTVR.QALKTNGT.SAL.TQ.GKAD.DS.EEEEE.KKAVVAVSKPGSGKK.KQN
Retrocopy SDDSIEEEEKEKPKGKGTVRLQALKTNGT<SALNTQKGKADGDSSEEEEE-KKAVVAVSKPGSGKKGKQN

Parental  EAAKEGETPQAKKIKPQTPNTFPKRKKGEKRASSPFRRIREEEIEVDARVADNSFDAKRGAAGDWGERAN
          EAAKE.ETPQAK.IKPQTPNTFP.RKKGEKRAS.PF.RIREEEIEVDARVADNSF.AK.G.AGDWGE.AN
Retrocopy EAAKEAETPQAKRIKPQTPNTFPRRKKGEKRASPPFQRIREEEIEVDARVADNSFNAKWGTAGDWGEHAN

Parental  QVLKFTKGKSFRHEKTKKKRGSYRGGSISVQVNSVKFDSE
          QVLKFTKGKSF..EKTKKKRGS.RGGSIS.QVNS.KFDSE
Retrocopy QVLKFTKGKSFQYEKTKKKRGSSRGGSISIQVNSIKFDSE

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	79.13 RPM
SRP017611_brain	0.00 RPM	53.35 RPM
SRP017611_kidney	0.00 RPM	43.32 RPM
SRP017611_liver	0.00 RPM	22.55 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1047 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1047 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1047 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010062	1 retrocopy	retro_cfam_1047 ,
Callithrix jacchus	ENSCJAG00000017832	2 retrocopies	retro_cjac_4136, retro_cjac_4187,
Homo sapiens	ENSG00000166197	1 retrocopy	retro_hsap_4781,
Nomascus leucogenys	ENSNLEG00000015012	1 retrocopy	retro_nleu_1101,
Pongo abelii	ENSPPYG00000002595	1 retrocopy	retro_pabe_3721,
Pan troglodytes	ENSPTRG00000023882	1 retrocopy	retro_ptro_3182,
Tursiops truncatus	ENSTTRG00000014974	1 retrocopy	retro_ttru_155,