RetrogeneDB ID: retro_cfam_396

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:54992122..54992581(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOPT1
• Ensembl ID: ENSCAFG00000030884
• Aliases: None
• Description: apoptogenic 1, mitochondrial [Source:HGNC Symbol;Acc:20492]

Sequence

>retro_cfam_396
CAGGTCTCAGGATTCTTGCCCTCCAAGAAAATCTAGCTGTGATTGGATAGGATCCCCCTCCAGGAAAAAATTCAAACTTC
GACCTGCCCACTTTTACATCCCCGAAAATGGCTCACCATTGTAACAAAAGCTAAGAGAATTAAGACAAGAAACACAAGAA
TGGAACCAACAGTCTGGGAAAACCAGAATTTGAGATTTCATAAGGAAAAGGAAGAATTTATTCACTCAAAATTAAAAGTT
AAAGGCCTGGAACTGAGAGTCAGATCAGGTCAAAAAGTAACATTAGCTCCAGAAGAAATGGCTGACTTTTATAAGGAACT
TTTAAGTAAAGATTTTCAGAAGCACATGTATTATAACAGGGATTGGTAGACGAGTAATTTTCCCATCACCTTCTTCTTGG
AAAAAATGGCCCTGGAGAGGGTTTGGAACAAGCTGATACTGAAACAAAAGAAGATGAGT

Alignment

ORF - retro_cfam_396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.19 %
• Parental protein coverage: 80.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KVSGF-CPPRKSCRDWIGPPD-KHSNLRPIHFYIPESESPLEQKLRQLRQETQEWNQQ-FWANQNLTFRK
          .VSGF.CPPRKS..DWIG.P..K...LRP.HFYIPE..SPL.QKLR.LRQETQEWNQQ..W.NQNL.F.K
Retrocopy QVSGF>CPPRKSSCDWIGSPSRKKFKLRPAHFYIPENGSPL*QKLRELRQETQEWNQQ<VWENQNLRFHK

Parental  EKEEFIHSRLKAKGLELRSGSGQKATLDAEEMADFYKEFLSKNFQKHMYYNRDWYKRNFAITFFMGKVAL
          EKEEFIHS.LK.KGLELR..SGQK.TL..EEMADFYKE.LSK.FQKHMYYNRDW...NF.ITFF..K.AL
Retrocopy EKEEFIHSKLKVKGLELRVRSGQKVTLAPEEMADFYKELLSKDFQKHMYYNRDW*TSNFPITFFLEKMAL

Parental  ERVWNKLRPKHKKSS
          ERVWNKL..K.KK.S
Retrocopy ERVWNKLILKQKKMS

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	0.04 RPM	20.92 RPM
SRP017611_brain	0.00 RPM	16.20 RPM
SRP017611_kidney	0.07 RPM	26.41 RPM
SRP017611_liver	0.00 RPM	9.35 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_396 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_396 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_396 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030884	2 retrocopies	retro_cfam_1514, retro_cfam_396 ,
Dasypus novemcinctus	ENSDNOG00000019553	5 retrocopies	retro_dnov_1003, retro_dnov_2304, retro_dnov_2391, retro_dnov_441, retro_dnov_777,
Erinaceus europaeus	ENSEEUG00000011728	1 retrocopy	retro_eeur_107,
Felis catus	ENSFCAG00000027939	3 retrocopies	retro_fcat_482, retro_fcat_549, retro_fcat_649,
Microcebus murinus	ENSMICG00000009792	1 retrocopy	retro_mmur_744,
Mustela putorius furo	ENSMPUG00000002350	2 retrocopies	retro_mputfur_1406, retro_mputfur_166,
Otolemur garnettii	ENSOGAG00000015416	1 retrocopy	retro_ogar_1394,