RetrogeneDB ID: retro_cfam_519

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:34783792..34784541(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS9
• Ensembl ID: ENSCAFG00000002122
• Aliases: None
• Description: mitochondrial ribosomal protein S9 [Source:HGNC Symbol;Acc:14501]

Sequence

>retro_cfam_519
CATTTCATTTTCTTTTATACTGGCAAACAGGCGTATTATTATTTATTAATGCATGAAGCATATGGAAAGCTACTAGAAGT
AGAAAAACGTCAGAATCAGTTGCAAGCCAAAGGTCTATTTTCAGAAAAAAACTAAAACCAAAGACCTGATTGGCAGCAGA
TGGCTGATTTAGGAAGAGCTAGAAGAAATGTTAGTGGAAAAACTGTCAGATCAAGATTATGCACAGTTCATTCGGCTGCT
AGAAGGGTTATTGACACTGCACTGTGGTTCCGAAGAAGAATTTGTGCAGAGATTTCGTAGGAGTGTAACTATCAATCAAA
AAAACAACTGATCGAACCTGTGCAATATGATGAGTAAGGAATGGCCTTCAGCACCAGCGAAGGTAAAAGAAAGAGTGTAA
AAACAGAAGCAATCATTTATGGGCATGGAAGTGGAAGAATAAAAGTAAATGGAATTGACTATCTTCTTTACTTCCCAGTG
ACACAAGACAAAGAACAGTTGATATTCCCCTTCCACTTCCTCGACCGGCTTGGAAAACACAACACAACCTGTACTGTCTC
CGGGGCGAGCAGTCATTGCAGGCTGGAGCCATACACTTGGCAGTGGTGAGAGCCTTGTGCAATTTCGTCACAGAGGAAGA
GGTCAAGTGGATGAGAGTAGCTGGACTGCTGACTGCTGATCCACACATCAAAGAATGGAAGAAGCCAGGCCAAGAGGGAG
CCTGAAGAAAGTTTACTTGGAAGAAGCGC

Alignment

ORF - retro_cfam_519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.54 %
• Parental protein coverage: 62.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HFLF-YTGKQAYYSL-MHEAYGKLLEVEKRQNQLQAKGLFSEK-TKTKDLIDSRWLIKEELEEMLVEKLS
          HF.F.YTGKQAYY.L.MHEAYGKLLEVEKRQNQLQAKGLFSEK.TKTKDLI.SRWLI.EELEEMLVEKLS
Retrocopy HFIFFYTGKQAYYYLLMHEAYGKLLEVEKRQNQLQAKGLFSEK>TKTKDLIGSRWLI*EELEEMLVEKLS

Parental  DQDYAQFIRLLERLLTLHCGSEEEFVQRFRRSVTI-QSKKQLIEPVQYDEQGMAFSTSEGKRKSAKAEAI
          DQDYAQFIRLLE.LLTLHCGSEEEFVQRFRRSVTI.QSKKQLIEPVQYDE.GMAFSTSEGKRKS.K.EAI
Retrocopy DQDYAQFIRLLEGLLTLHCGSEEEFVQRFRRSVTI<QSKKQLIEPVQYDE*GMAFSTSEGKRKSVKTEAI

Parental  VYGHGSGRIKVNGIDYLLYFPVTQDREQLMFPFHFLDRLGKHDTTCTVSG-GGRSSQAGAIRLAVARALC
          .YGHGSGRIKVNGIDYLLYFPVTQD.EQL.FPFHFLDRLGKH.TTCTVSG.G..S.QAGAI.LAV.RALC
Retrocopy IYGHGSGRIKVNGIDYLLYFPVTQDKEQLIFPFHFLDRLGKHNTTCTVSG<GEQSLQAGAIHLAVVRALC

Parental  SFVTEEEVEWMRQAGLLTADPRVKERKKPGQEGARRKFTWKKR
          .FVTEEEV.WMR.AGLLTADP..KE.KKPGQEGA.RKFTWKKR
Retrocopy NFVTEEEVKWMRVAGLLTADPHIKEWKKPGQEGA*RKFTWKKR

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	31.50 RPM
SRP017611_brain	0.00 RPM	30.25 RPM
SRP017611_kidney	0.00 RPM	89.68 RPM
SRP017611_liver	0.07 RPM	30.31 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_519 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_519 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_519 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002122	1 retrocopy	retro_cfam_519 ,
Callithrix jacchus	ENSCJAG00000008156	1 retrocopy	retro_cjac_40,
Otolemur garnettii	ENSOGAG00000007255	1 retrocopy	retro_ogar_3314,
Pteropus vampyrus	ENSPVAG00000000927	1 retrocopy	retro_pvam_963,