RetrogeneDB ID: retro_cfam_1557

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 34:34473662..34474530(-)
• Located in intron of: None

Retrocopy information

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

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_1557
ACAGCCTCCTCAGCCAAGGACCCTTGGTTCTGTGAGTCTGGGGATGCTCTATACACTTGTTCAGTGGGGAAGGATGGCGA
GGAGCAGGCAACCTCAGGGCAGAGACGAAAGCAGGGGAGCCCCAGAGAATGCAATGTGAAGATGAAAAAGAAATAGAAAA
TCCACCAGAAGGGAGATACTGCTCTGGGGCACCTTGAGTGCTCCAAGTCCATAGGGAGAAGCCCTAGGAAAGGAAGTAAG
AAGCCAGTCAAAACTGAGCCTCCAGAATATATCCCAATAGGACATAACCCCAAACCCCTGCAAAGAAGAAAATGAAGTCC
AAGAAAAAGAGCCACCAGGGATTGAGGAACCAGCTCTGAAGAGGAATAAAAACAAGGGGAGAGAAGAGTAGCAGGAGAAT
CTTGGGAAGAAGAGCCTGACACAGACTTAGAGGTGGTGTTGGAAAAGAAAGGCAACATGGATGAGGCGCACATAGACCAG
GTGAGGCGAAAGGCCTTGCAAGAAGAGATCGATTGTGAGTCAGGCAAAACCAGAAGTTTCTGAACCAAAGAAGTAGACAG
GAACTCAGTTTGGCCAGTGGGATACTGCTGGTTTTGAAAATGAGAAACAGAAACTGAAATTTCTCAAACTTATGGGCGGC
TTTAAAAACGTGTCCCCTTCACTCAGCCGCCCCCCTAACACAACTGGAAGGCCCAACGTGGGTCTCAGCAAGAAGGCAGC
AATTGCCCTGCAGCAGAACCTGCAGCAGGACTATGACCGGGCCATGACTTGGAAGTACAGGCGTGGTGCTGGCCTCGGCT
TCTCCTCCACTCCAGACAAAATCTTTTGTATTGACAGGAATGCTTCCAAGTCCATCAAATTTGAAGAT

Alignment

ORF - retro_cfam_1557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.51 %
• Parental protein coverage: 63.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TASSAKDPWFYESGDALYTCSVGKDGEEQATSGQKRKQGSPRECNVKMKKKKKIHQKGDTSLGHLECSKS
          TASSAKDPWF.ESGDALYTCSVGKDGEEQATSGQ.RKQGSPRECNVKMKKK.KIHQKGDT.LGHLECSKS
Retrocopy TASSAKDPWFCESGDALYTCSVGKDGEEQATSGQRRKQGSPRECNVKMKKK*KIHQKGDTALGHLECSKS

Parental  VERSPRKGSKKLVKIEAPEYIPIGHNPK-TPAKKKMKSKKKT-EQPGIEEPALKRNK-KKGKESRVAGES
          ..RSPRKGSKK.VK.E.PEYIPIGHNPK.TPAKKKMKS.KK..E.PGIEEPALKRNK.K.G.E.RVAGES
Retrocopy IGRSPRKGSKKPVKTEPPEYIPIGHNPK<TPAKKKMKS-KKK<EPPGIEEPALKRNK<KQG-ERRVAGES

Parental  WEEEPDTDLEVVLEKKGNMDEAHIDQVRRKALQEEIDRESGKT-EVSEPKKWTGTQFGQWDTAGFENEEQ
          WEEEPDTDLEVVLEKKGNMDEAHIDQVRRKALQEEID.ESGKT.EVSEPKK.TGTQFGQWDTAGFENE.Q
Retrocopy WEEEPDTDLEVVLEKKGNMDEAHIDQVRRKALQEEIDCESGKT>EVSEPKK*TGTQFGQWDTAGFENEKQ

Parental  KLKFLKLMGGFKNMSPSFSRPSNTIGRPNMALNKKAADALQQNLQQDYDRAMSWKYKRGAGLGFSSAPDK
          KLKFLKLMGGFKN.SPS.SRP.NT.GRPN..L.KKAA.ALQQNLQQDYDRAM.WKY.RGAGLGFSS.PDK
Retrocopy KLKFLKLMGGFKNVSPSLSRPPNTTGRPNVGLSKKAAIALQQNLQQDYDRAMTWKYRRGAGLGFSSTPDK

Parental  IFYIDRNASKSIKFED
          IF.IDRNASKSIKFED
Retrocopy IFCIDRNASKSIKFED

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	0.13 RPM	23.48 RPM
SRP017611_brain	0.00 RPM	10.48 RPM
SRP017611_kidney	0.00 RPM	14.33 RPM
SRP017611_liver	0.00 RPM	9.06 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1557 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1557 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,