RetrogeneDB ID: retro_cfam_1376

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:40225683..40226493(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000013279
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1376
GCGGCGGAGGAGCCTCAGCAGCAGAAGCAGGAGCCGCTCGGCAGCGACTCCGAAGGTGTTAACTGTCTTGCTTATGATGA
AGCCATCATGGCTCAGCAGGACCGAATTCAGCAAGAGATTGCTGTGCAGAACCCTCTGGTCTCAGAGCGGCTGGAGCTTT
CGGTCCTGTACAAGGAGTATGCTGAGGATGACAACATCTATCAACAGAAGATCAAGGACCTCCACAAAAAGTACTCCTAC
ATCCGCAAGACCAGGCCTGATGGAAACTGTTTCTACCGAGCTTTCGGATTCTCCCACTTGGAGGCGCTGCTGGATGACAG
CAAGGAATTGCAGCGGTTTAAGGCTGTGTCTGCCAAGAGCAAAGAGGACCTGGTGTCCCAGGGCTTCACTGAATTCACAA
TCGAGGATTTCCACAACACGTTCATGGACCTGATCGAGCAGGTGGAGAAGCAGACCTCTGTAGCTGACCTGCTGGCCTCC
TTCAACGACCAGAGTACCTCGGACTACCTGGTGGTGTACCTGCGGCTGCTCACCTCCGGCTACCTGCAGCGCGAGAGCAA
GTTCTTCGAGCACTTCATCGAGGGCGGGCGGACAGTCAAGGAGTTCTGCCAGCAGGAGGTGGAGCCCATGTGCAAGGAGA
GCGACCACATTCACATCATCGCACTGGCCCAGGCTCTGAGCGTCTCCATCCAGGTGGAGTACATGGACCGCGGCGAGGGC
GGCACCACCAACCCGCACATCTTCCCCGAGGGCTCTGAGCCCAAGGTGTACCTTCTCTACCGGCCTGGACACTACGATAT
CCTCTACAAA

Alignment

ORF - retro_cfam_1376 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.78 %
• Parental protein coverage: 99.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAEEPQQQKQELFGFLLPGVNCLAYDEAIMAQQDRIQQEIAVQNPLVSERLELSVLYKEYAEDDNIYQQK
          AAEEPQQQKQE..G....GVNCLAYDEAIMAQQDRIQQEIAVQNPLVSERLELSVLYKEYAEDDNIYQQK
Retrocopy AAEEPQQQKQEPLGSDSEGVNCLAYDEAIMAQQDRIQQEIAVQNPLVSERLELSVLYKEYAEDDNIYQQK

Parental  IKDLHKKYSYIRKTRPDGNCFYRAFGFSHLEALLDDSKELQRFKAVSAKSKEDLVSQGFTEFTIEDFHNT
          IKDLHKKYSYIRKTRPDGNCFYRAFGFSHLEALLDDSKELQRFKAVSAKSKEDLVSQGFTEFTIEDFHNT
Retrocopy IKDLHKKYSYIRKTRPDGNCFYRAFGFSHLEALLDDSKELQRFKAVSAKSKEDLVSQGFTEFTIEDFHNT

Parental  FMDLIEQVEKQTSVADLLASFNDQSTSDYLVVYLRLLTSGYLQRESKFFEHFIEGGRTVKEFCQQEVEPM
          FMDLIEQVEKQTSVADLLASFNDQSTSDYLVVYLRLLTSGYLQRESKFFEHFIEGGRTVKEFCQQEVEPM
Retrocopy FMDLIEQVEKQTSVADLLASFNDQSTSDYLVVYLRLLTSGYLQRESKFFEHFIEGGRTVKEFCQQEVEPM

Parental  CKESDHIHIIALAQALSVSIQVEYMDRGEGGTTNPHIFPEGSEPKVYLLYRPGHYDILYK
          CKESDHIHIIALAQALSVSIQVEYMDRGEGGTTNPHIFPEGSEPKVYLLYRPGHYDILYK
Retrocopy CKESDHIHIIALAQALSVSIQVEYMDRGEGGTTNPHIFPEGSEPKVYLLYRPGHYDILYK

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	6.64 RPM	36.03 RPM
SRP017611_brain	5.16 RPM	42.87 RPM
SRP017611_kidney	3.57 RPM	19.75 RPM
SRP017611_liver	0.44 RPM	4.57 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1376 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1376 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1376 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,