RetrogeneDB ID: retro_cfam_125

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:42646361..42647903(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000015958
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: USP22
• Ensembl ID: ENSCAFG00000018523
• Aliases: None
• Description: ubiquitin specific peptidase 22 [Source:HGNC Symbol;Acc:12621]

Sequence

>retro_cfam_125
GAACTGCGGGTGATCTACCAGTGCTTCGTGTGGTGTGGAACCCCAGAGACCAGGAAAAGCAAGGCAAAGTCGTGCATCTG
CCATGTGTGTGGCACCCATTTGAACAGACTTCACTCTTGCCTTTCCTGTGTCTTCTTTGGCTGCTTCACCGAGAAACACA
TTCACGAGCACGCCGAGACAAAACAACACAACTTAGCCGTAGACCTTTATTACGGAGGTATATACTGCTTTATGTGTAAG
GATTATGTGTATGACAAAGACATTGAGCAAATTGCCAAAGAAGAGCAAGGAGAAGCTTTGAAATTACAAGCCTCCACCTC
AACCGAGGTTTCTCACCAGCAGTGTTCAGTGATGGGACTCGGTGAGAAATATCCAACCTGGGAGATGACCAAACCCGAGT
TAGAACTGCTGGGGTACAATCCGAGGAGAAGAAGGATCACCTCCAGCTTTACCATCGGTCTGAGAGGACTGATCAATCTT
GGCAACACGTGCTTTATGAACTGCATCGTCCAGGCCCTTACCCATACTCCCATACTGAGAGATTTCTTCCTCTCTGACAG
GCACAGGTGTGAGATGCCGAGTCCTGAGCTGTGTCTGGTCTGCGAGATGTCTTCACTCTTTCGGGAGTTGTACTCTGGAA
ACCCGTCTCCTCACGTTCCTTATAAGTTGCTGCACCTGGTATGGATACATGCACGCCACTTAGCAGGGTACAGGCAGCAG
GATGCCCACGAATTCCTCATTGCAGCCTTAGACGTCCTGCACAGGCACTGCAAAGGCGATGATGCTGGGAAAGCTGCCAA
CAATCCCAACCACTGTAACTGCATCATAGACCAAATCTTCACAGGTGGCCTGCAGTCGGATGTCACCTGTCAAGCCTGCC
ATGGTGTCTCCACCACCATAGACCCATGCTGGGACATCAGTTTGGACTTGCCTGGCTCGTGCACCTCCTTCTGGCCCATG
AGCCCAGGGAGGGAGAGCAGTGTGAATGGGGAGAGCCACATCCCAGGAATCACCACCCTCACAGACTGCTTGCGAAGGTT
TACAAGGCCAGAGCACTTGGGAAGCAGTGCCAAAATCAAGTGCGGTAGTTGCCAAAGCTACCAGGAGTCTACCAAGCAAC
TCACGATGAATAAATTACCTGTTGTTGCCTGTTTTCATTTCAAACGGTTCGAACACTCTGCCAAACAGAGGCGCAAGATC
ACTACATATATATCCTTTCCTCTGGAGCTGGATATGACCCCATTTATGGCCTCAAGTAAAGAGAGTAGGATGAATGGACA
GTTGCAGCTGCCAACCAATAGTGGAAACGACGAGAATAAGTATTCCTTGTTTGCTGTGGTTAATCACCAAGGAACCTTGG
AGAGCGGCCATTACACCAGCTTCATCCGGCACCACAAGGACCAGTGGTTCAAGTGTGATGATGCCGTCATCACCAAGGCC
AGTATTAAGGACGTGCTGGACAGTGAAGGGTATTTACTGTTCTATCACAAACAGGTCCTGGAGCACGAGTCAGAAAAAGT
GAAAGAAATGAATACACAAGCC

Alignment

ORF - retro_cfam_125 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.09 %
• Parental protein coverage: 84.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEQRKAWKMQGVGEKFSTWEPTKRELELLKHNPKRRKITSNCTIGLRGLINLGNTCFMNCIVQALTHTPL
          E.........G.GEK..TWE.TK.ELELL..NP.RR.ITS..TIGLRGLINLGNTCFMNCIVQALTHTP.
Retrocopy EVSHQQCSVMGLGEKYPTWEMTKPELELLGYNPRRRRITSSFTIGLRGLINLGNTCFMNCIVQALTHTPI

Parental  LRDFFLSDRHRCEMQSPSSCLVCEMSSLFQEFYSGHRSPHIPYKLLHLVWTHARHLAGYEQQDAHEFLIA
          LRDFFLSDRHRCEM.SP..CLVCEMSSLF.E.YSG..SPH.PYKLLHLVW.HARHLAGY.QQDAHEFLIA
Retrocopy LRDFFLSDRHRCEMPSPELCLVCEMSSLFRELYSGNPSPHVPYKLLHLVWIHARHLAGYRQQDAHEFLIA

Parental  ALDVLHRHCKGDDNGKKANNPNHCNCIIDQIFTGGLQSDVTCQVCHGVSTTIDPFWDISLDLPGSSTPFW
          ALDVLHRHCKGDD.GK.ANNPNHCNCIIDQIFTGGLQSDVTCQ.CHGVSTTIDP.WDISLDLPGS.T.FW
Retrocopy ALDVLHRHCKGDDAGKAANNPNHCNCIIDQIFTGGLQSDVTCQACHGVSTTIDPCWDISLDLPGSCTSFW

Parental  PLSPGSEGSVVNGESHVAGTTTLTDCLRRFTRPEHLGSSAKIKCSGCHSYQESTKQLTMKKLPIVACFHL
          P.SPG.E.S.VNGESH..G.TTLTDCLRRFTRPEHLGSSAKIKC..C.SYQESTKQLTM.KLP.VACFH.
Retrocopy PMSPGRESS-VNGESHIPGITTLTDCLRRFTRPEHLGSSAKIKCGSCQSYQESTKQLTMNKLPVVACFHF

Parental  KRFEHSAKLRRKITTYVSFPLELDMTPFMASSKESRMNGQYQQPTDSLNNDNKYSLFAVVNHQGTLESGH
          KRFEHSAK.RRKITTY.SFPLELDMTPFMASSKESRMNGQ.Q.PT.S.N..NKYSLFAVVNHQGTLESGH
Retrocopy KRFEHSAKQRRKITTYISFPLELDMTPFMASSKESRMNGQLQLPTNSGNDENKYSLFAVVNHQGTLESGH

Parental  YTSFIRQHKDQWFKCDDAIITKASIEDVLDSEGYLLFYHKQFLEYE
          YTSFIR.HKDQWFKCDDA.ITKASI.DVLDSEGYLLFYHKQ.LE.E
Retrocopy YTSFIRHHKDQWFKCDDAVITKASIKDVLDSEGYLLFYHKQVLEHE

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	3.74 RPM	154.81 RPM
SRP017611_brain	11.83 RPM	119.88 RPM
SRP017611_kidney	7.79 RPM	33.75 RPM
SRP017611_liver	0.36 RPM	23.42 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_125 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_125 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_125 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008978	1 retrocopy	retro_btau_82,
Canis familiaris	ENSCAFG00000018523	1 retrocopy	retro_cfam_125 ,
Homo sapiens	ENSG00000124422	1 retrocopy	retro_hsap_26,
Microcebus murinus	ENSMICG00000009998	1 retrocopy	retro_mmur_1,
Mus musculus	ENSMUSG00000042506	1 retrocopy	retro_mmus_239,
Otolemur garnettii	ENSOGAG00000015801	1 retrocopy	retro_ogar_274,
Pan troglodytes	ENSPTRG00000008891	1 retrocopy	retro_ptro_44,
Pteropus vampyrus	ENSPVAG00000001934	1 retrocopy	retro_pvam_905,
Ictidomys tridecemlineatus	ENSSTOG00000023814	1 retrocopy	retro_itri_163,