RetrogeneDB ID: retro_cfam_1763

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:42884540..42885901(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000018533
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KNOP1
• Ensembl ID: ENSCAFG00000018032
• Aliases: None
• Description: lysine-rich nucleolar protein 1 [Source:HGNC Symbol;Acc:34404]

Sequence

>retro_cfam_1763
ATGATCACCAAAACCCACAAAGGAGACCTGACCTTGGGCTCCCAGAGAAAAAGAAGAAAAAGAAGAAGGTGGTCAAAGAA
CCAGAGACTCAATACTCAGTTTTAAACAGTGATACTTATTTCAGTGAGATCTGTTCCACAAGAGCCACATCCCCTTCAAA
GAGTGTGGTCCTAGAGCAGGCATCTGAGATGCCTCTAGTGAAGAAAAAGAAGGGCCATAGCACCCTCTGTGAGGAGTGCC
TAGAACCTGAGACTGTGTTACGTGCTGGACGGACAGGGAAGTTGTCTAGCTCCAGCAGGCAGGCTCTTGGTTCATCTGAG
TTTCAAGGTGGGAAGAAGAAAAAGAAGAGAAAGTCCTTATGGCCTCTGGCCATGCCCCCTGCCTCAAGAGTGAAGACCTC
CCCAGACCCCAAAGAGGACGAGGAGGTGACCAGAGTTGGCAAGAAACCCAAAAAGCACAAGAAGGAGAAAAAGACCCAGG
AGGCTACAGCCTCCTCAGCCAAGGACCCTTGGTTCTGTGAGTCTGGGGATGCTCTATACACTTGTTCAGTGAGGAAGGAT
GGCGAGGAACAGGCAACCTCAGGGCAGAAACGAAAGCAGGGGAGCCCCAGAGAATGCAATGTGAAGATGAAGAAGAAAAA
GAAAATCCACCAGAAGGGAGATACTTCTCTAGGGCACCGTGAGTGCTCTAAGTCTGTAGAGAGAAGCCCTAGGAAAGGAA
GTAAGAAGCCAGTCAAAATTGAGGCTCCAGAATATATCCCAATAGGACATAACCCCAAACCCCCTGCCAAGAAGAAAATG
AAGTCCAAGAAAAAGACAGAGCAGCCAGGGATTGAGGAACCAGCTCTGAAGAGGAATAAAAAGAAGCGGAAAGAGAGCAG
AGTAGCGGGAGAATCTTGGGAAGAGGAGCCTGACACAGACTTAGAGGTGGTGTTGGAAAAGAAAGGCACCATGGATGAGG
CACACATGGACCAGGTGAGGCGAAAGGCCTTGCAAGAAGAGATCGATCATGAGTCAGGCAAAACAGAAGTTTCTGAACCA
AAGAAGTGGACAGGAACTCAGTTTGGCCAGTGGGATACTGCTGGTTTTGAAAACGAGGAACAGAAATTGAAATTTCTCAA
ACTTATGGGTGGCTTTAAAAACGTGTCCCCTTCATCCAGCCACCCCTCTAACACATTTGGAAGGCCCAACATGACTCTCA
ACAAGAAGGCAGCCGACACCCTGCAGCAGAACCTGCAGCAGGACTATGACCGGGCCATGAGCTGGAAGTACAAGCGTGGT
GCTGGCCTCGGCTTCTCCTCTGCTCCAGACAAAATCTTTTATATTGACAGGAATGCTTCCAAGTCCATCAAGTTTGAAGA
T

Alignment

ORF - retro_cfam_1763 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MITKTHKGDL-GLGLPEKKKKKKKVVKEPETQYSVLNSDAYFSEICSTRATSPSKSVVLEQASEMPLMKK
          MITKTHKGDL..LGLP........VVKEPETQYSVLNSD.YFSEICSTRATSPSKSVVLEQASEMPL...
Retrocopy MITKTHKGDL<DLGLPXXXXXXXXVVKEPETQYSVLNSDTYFSEICSTRATSPSKSVVLEQASEMPLV--

Parental  KKKKKGHSTLCEECLEPETVLRAGWTGKLSSSRKQALGSSEFQGGEKKKKRKSLRPLAMSPASRVKISPD
          .KKKKGHSTLCEECLEPETVLRAG.TGKLSSS..QALGSSEFQGG.KKKKRKSL.PLAM.PASRVK.SPD
Retrocopy -KKKKGHSTLCEECLEPETVLRAGRTGKLSSSSRQALGSSEFQGGKKKKKRKSLWPLAMPPASRVKTSPD

Parental  PKEDEEVTRVGKKPKKHKKEKKTQEATASSAKDPWFYESGDALYTCSVGKDGEEQATSGQKRKQGSPREC
          PKEDEEVTRVGKKPKKHKKEKKTQEATASSAKDPWF.ESGDALYTCSV.KDGEEQATSGQKRKQGSPREC
Retrocopy PKEDEEVTRVGKKPKKHKKEKKTQEATASSAKDPWFCESGDALYTCSVRKDGEEQATSGQKRKQGSPREC

Parental  NVKMKKKKKIHQKGDTSLGHLECSKSVERSPRKGSKKLVKIEAPEYIPIGHNPKTPAKKKMKSKKKTEQP
          NVKMKKKKKIHQKGDTSLGH.ECSKSVERSPRKGSKK.VKIEAPEYIPIGHNPK.PAKKKMKSKKKTEQP
Retrocopy NVKMKKKKKIHQKGDTSLGHRECSKSVERSPRKGSKKPVKIEAPEYIPIGHNPKPPAKKKMKSKKKTEQP

Parental  GIEEPALKRNKKKGKESRVAGESWEEEPDTDLEVVLEKKGNMDEAHIDQVRRKALQEEIDRESGKTEVSE
          GIEEPALKRNKKK.KESRVAGESWEEEPDTDLEVVLEKKG.MDEAH.DQVRRKALQEEID.ESGKTEVSE
Retrocopy GIEEPALKRNKKKRKESRVAGESWEEEPDTDLEVVLEKKGTMDEAHMDQVRRKALQEEIDHESGKTEVSE

Parental  PKKWTGTQFGQWDTAGFENEEQKLKFLKLMGGFKNMSPSFSRPSNTIGRPNMALNKKAADALQQNLQQDY
          PKKWTGTQFGQWDTAGFENEEQKLKFLKLMGGFKN.SPS.S.PSNT.GRPNM.LNKKAAD.LQQNLQQDY
Retrocopy PKKWTGTQFGQWDTAGFENEEQKLKFLKLMGGFKNVSPSSSHPSNTFGRPNMTLNKKAADTLQQNLQQDY

Parental  DRAMSWKYKRGAGLGFSSAPDKIFYIDRNASKSIKFED
          DRAMSWKYKRGAGLGFSSAPDKIFYIDRNASKSIKFED
Retrocopy DRAMSWKYKRGAGLGFSSAPDKIFYIDRNASKSIKFED

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	1.05 RPM	23.48 RPM
SRP017611_brain	3.49 RPM	10.48 RPM
SRP017611_kidney	0.20 RPM	14.33 RPM
SRP017611_liver	0.07 RPM	9.06 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1763 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1763 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1763 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018032	2 retrocopies	retro_cfam_1557, retro_cfam_1763 ,
Callithrix jacchus	ENSCJAG00000009625	1 retrocopy	retro_cjac_3199,
Homo sapiens	ENSG00000103550	3 retrocopies	retro_hsap_3487, retro_hsap_4007, retro_hsap_979,
Gorilla gorilla	ENSGGOG00000005673	1 retrocopy	retro_ggor_2691,
Macaca mulatta	ENSMMUG00000002707	2 retrocopies	retro_mmul_1771, retro_mmul_798,
Nomascus leucogenys	ENSNLEG00000012496	2 retrocopies	retro_nleu_1618, retro_nleu_551,
Otolemur garnettii	ENSOGAG00000010065	4 retrocopies	retro_ogar_1115, retro_ogar_1480, retro_ogar_1481, retro_ogar_2259,
Pongo abelii	ENSPPYG00000007151	3 retrocopies	retro_pabe_3293, retro_pabe_828, retro_pabe_920,
Pan troglodytes	ENSPTRG00000007836	3 retrocopies	retro_ptro_2360, retro_ptro_767, retro_ptro_924,