RetrogeneDB ID: retro_cfam_2064

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:39412672..39413017(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NPM3
• Ensembl ID: ENSCAFG00000009919
• Aliases: None
• Description: nucleophosmin/nucleoplasmin 3 [Source:HGNC Symbol;Acc:7931]

Sequence

>retro_cfam_2064
GTCACTATGGACAGTTTTTCCTTTGGCTGTTAGCTCTCTAGCCATACCCGCTCTTTCACCTTGAAGGTAGAGGAAGAGGA
TGAGGTGGAGCACTTGCTGGCTTTGGCCATGCTCTGCCTCACCAAGAGGGCTGAAGAGGAATGTAATGTGGTAGAAGTCA
TGGCCAGGAAGCATTACCACCAAGAGATTGCTGTCCCTGTGGCCAACCTCAAGTTGTCCTGCCAATTCATGTTTAGTTTG
GATGACCTCCAGCTCCAACCACCTGTAACCTTCTGTCTGAAATCAGGTTCTGGCCCCATGTAAATTGCTGGGCAGCACCA
GATTGTTTCTATAAGCAATGATGTT

Alignment

ORF - retro_cfam_2064 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.13 %
• Parental protein coverage: 56.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTMDSFFFGCELSGHTRSFTFKVEEEDDAEHVLALTMLCLTEGAKDECNVVEVVARNHDHQEIAVPVANL
          VTMDSF.FGC.LS.HTRSFT.KVEEED..EH.LAL.MLCLT..A..ECNVVEV.AR.H.HQEIAVPVANL
Retrocopy VTMDSFSFGC*LSSHTRSFTLKVEEEDEVEHLLALAMLCLTKRAEEECNVVEVMARKHYHQEIAVPVANL

Parental  KLSCQPMLSLDDFQLQPPVTFRLKSGSGPVRITGRHQIVTISNDV
          KLSCQ.M.SLDD.QLQPPVTF.LKSGSGP..I.G.HQIV.ISNDV
Retrocopy KLSCQFMFSLDDLQLQPPVTFCLKSGSGPM*IAGQHQIVSISNDV

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	15.79 RPM
SRP017611_brain	0.00 RPM	6.27 RPM
SRP017611_kidney	0.00 RPM	41.87 RPM
SRP017611_liver	0.00 RPM	14.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2064 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2064 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2064 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017639	2 retrocopies	retro_amel_1233, retro_amel_90,
Bos taurus	ENSBTAG00000016335	1 retrocopy	retro_btau_1164,
Canis familiaris	ENSCAFG00000009919	2 retrocopies	retro_cfam_1968, retro_cfam_2064 ,
Canis familiaris	ENSCAFG00000016912	3 retrocopies	retro_cfam_22, retro_cfam_286, retro_cfam_900,
Callithrix jacchus	ENSCJAG00000017650	2 retrocopies	retro_cjac_2491, retro_cjac_3052,
Cavia porcellus	ENSCPOG00000006301	1 retrocopy	retro_cpor_1315,
Dasypus novemcinctus	ENSDNOG00000018876	1 retrocopy	retro_dnov_1279,
Dipodomys ordii	ENSDORG00000003491	1 retrocopy	retro_dord_577,
Felis catus	ENSFCAG00000007178	1 retrocopy	retro_fcat_1906,
Homo sapiens	ENSG00000107833	1 retrocopy	retro_hsap_792,
Macropus eugenii	ENSMEUG00000003465	2 retrocopies	retro_meug_20, retro_meug_25,
Microcebus murinus	ENSMICG00000011739	1 retrocopy	retro_mmur_126,
Myotis lucifugus	ENSMLUG00000004961	1 retrocopy	retro_mluc_2333,
Macaca mulatta	ENSMMUG00000015774	1 retrocopy	retro_mmul_1072,
Mus musculus	ENSMUSG00000056209	2 retrocopies	retro_mmus_2756, retro_mmus_3479,
Ochotona princeps	ENSOPRG00000009229	2 retrocopies	retro_opri_1019, retro_opri_92,
Pongo abelii	ENSPPYG00000002589	1 retrocopy	retro_pabe_706,
Pan troglodytes	ENSPTRG00000002875	1 retrocopy	retro_ptro_551,