RetrogeneDB ID: retro_cfam_2023

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: JH373239.1:706956..707542(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OTUB1
• Ensembl ID: ENSCAFG00000014729
• Aliases: None
• Description: Canis lupus familiaris OTU domain, ubiquitin aldehyde binding 1 (OTUB1), mRNA. [Source:RefSeq mRNA;Acc:NM_001251947]

Sequence

>retro_cfam_2023
CTCCACAAAAGCACTCCTACATCCGCAAGACCAGGCGCGAGCAAACTGTTTCTACGGAGCTTCGGGATTCTCCCACCTGG
AGGCGCTGCCGGATGACAGCGAGGAATTGCAGCGCTTTGAGGCTGTGTCTGCCAAGGGCCAAGAGGCCCTGGTGTCCAGG
GCTTCCCTGAGGCCACAATCGAGGATTTCCACAGCACGTTCGTGGGCCTGATGGAGCGGGTGGAGAAGCAGACCTCTGTA
GCTGACCTGCTGGCCTCCTTCCACGGCCACAGCACCTCGGACTACCTGGTGGTGTACCTGCGGCTGCTCACCTCCGGCTC
CCTGCAGTGCCAGAGCAAGTTCTTCAGCACTTCCTGGAGGGCGGGCGGACAGTCCAGGAGTTCTGTCAGCAGGAGGTGGA
GCCCACGTGCAAGGAGAGCGACCACATTCACTCCACCGCACTGGCCCAGGCCCTGAGCGTCTCCGTCCAGGTGGAGCACA
TGGACCGCGCGAGGGCGGCACCACCAACCCGCACACCTTCCCCGAGGGCTCTGAGCCCAAGGTGTACCTTCTCTGCCGGC
CTGGGCACTACCATATCCTCTACAAA

Alignment

ORF - retro_cfam_2023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.21 %
• Parental protein coverage: 72.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LHK-KYSYIRKTRPD-GNCFYRAFGFSHLEALLDDSKELQRFKAVSAKSKEDLVS-QGFTEFTIEDFHNT
          LHK.K.SYIRKTR....NCFY.A.GFSHLEAL.DDS.ELQRF.AVSAK..E.LVS.QGF.E.TIEDFH.T
Retrocopy LHK<KHSYIRKTRRE<ANCFYGASGFSHLEALPDDSEELQRFEAVSAKGQEALVS<QGFPEATIEDFHST

Parental  FMDLIEQVEKQTSVADLLASFNDQSTSDYLVVYLRLLTSGYLQRESKFF-EHFIEGGRTVKEFCQQEVEP
          F..L.E.VEKQTSVADLLASF...STSDYLVVYLRLLTSG.LQ..SKFF..HF.EGGRTV.EFCQQEVEP
Retrocopy FVGLMERVEKQTSVADLLASFHGHSTSDYLVVYLRLLTSGSLQCQSKFF<QHFLEGGRTVQEFCQQEVEP

Parental  MCKESDHIHIIALAQALSVSIQVEYMDRG-EGGTTNPHIFPEGSEPKVYLLYRPGHYDILYK
          .CKESDHIH..ALAQALSVS.QVE.MDR..EGGTTNPH.FPEGSEPKVYLL.RPGHY.ILYK
Retrocopy TCKESDHIHSTALAQALSVSVQVEHMDRA<EGGTTNPHTFPEGSEPKVYLLCRPGHYHILYK

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	0.17 RPM	36.03 RPM
SRP017611_brain	1.59 RPM	42.87 RPM
SRP017611_kidney	0.00 RPM	19.75 RPM
SRP017611_liver	0.00 RPM	4.57 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2023 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2023 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2023 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018084	1 retrocopy	retro_amel_1270,
Bos taurus	ENSBTAG00000003967	1 retrocopy	retro_btau_1119,
Canis familiaris	ENSCAFG00000014729	2 retrocopies	retro_cfam_1376, retro_cfam_2023 ,
Equus caballus	ENSECAG00000002621	1 retrocopy	retro_ecab_760,
Myotis lucifugus	ENSMLUG00000012235	2 retrocopies	retro_mluc_1257, retro_mluc_614,
Mustela putorius furo	ENSMPUG00000013314	1 retrocopy	retro_mputfur_1057,
Pteropus vampyrus	ENSPVAG00000017099	2 retrocopies	retro_pvam_131, retro_pvam_274,
Rattus norvegicus	ENSRNOG00000021175	1 retrocopy	retro_rnor_2431,
Sarcophilus harrisii	ENSSHAG00000004156	1 retrocopy	retro_shar_87,