RetrogeneDB ID: retro_cfam_676

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:12732839..12733286(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NME1
• Ensembl ID: ENSCAFG00000023628
• Aliases: NME1, NM23-C1, NM23A
• Description: Canis lupus familiaris non-metastatic cells 1, protein (NM23A) expressed in (NME1), mRNA. [Source:RefSeq mRNA;Acc:NM_001024637]

Sequence

>retro_cfam_676
AGGGCAGTGGCCAACGCAGAGCACACGGCCACTGCCAACAAGCCGGAGGGCCTGCAGCACAGCCTAGTGGCTTAGGTCAT
CGAGCACTTGGAGCAGAAAGGATTCCTCCTGTGGCCACACAGTTCCTTAGGCCTCTGAGGAGCACCTGAAGCAGCCCTGC
ATTGACCTGAAAGACCGTCCACTCTGTCTGGGGCTTCAGACATATATGAATGAGGGCGCGTTGTGGCCGTGGTCTGGGAA
GGGCTGAAGATGCCCAGACAGGGGCCTGGGGAGACCAGTCCAGTGGGCCCTAAGCTGGCCACCACTCACGGGGACTTCAG
CGCTCGCGCTGGAAGAGCATCATTCCTAGTGGCGATTCAGTAAAACCTGATGAAAAGAAATCGGCCTACAGCTAAAGCCC
AAAGAACTGGTGATTACAAGTCTTGTACTTTGGACCAGATCTATGAA

Alignment

ORF - retro_cfam_676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.12 %
• Parental protein coverage: 52.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RAMAHQERTFIAIKPDGVQRGLVGDIVKRFEQKGFRL-VAMKFLR-ASEDLLKEHYIDLKDRPFYPGLVK
          RA.A..E.T..A.KP.G.Q..LV.......EQKGF.L.VA..FLR.ASE..LK...IDLKDRP...GL..
Retrocopy RAVANAEHTATANKPEGLQHSLVA*VIEHLEQKGFLL<VATQFLR<ASEEHLKQPCIDLKDRPLCLGLQT

Parental  YMHSGP-VVAMVWEGLNVVKTGRMMLGETNPADSKPGTIRGDFCIQVGR-NIIHGSDSVKSAE-KEISLW
          YM..G..VVA.VWEGL.....G....GET.P...K..T..GDF....GR..II...DSVK..E.KEI.L.
Retrocopy YMNEGA<VVAVVWEGLKMPRQGP---GETSPVGPKLATTHGDFSARAGR<SIIPSGDSVKPDE<KEIGLQ

Parental  FKPEELV-DYKSCAFDWIYE
          .KP.ELV.DYKSC..D.IYE
Retrocopy LKPKELV<DYKSCTLDQIYE

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	94.92 RPM
SRP017611_brain	0.16 RPM	88.05 RPM
SRP017611_kidney	0.00 RPM	357.59 RPM
SRP017611_liver	0.00 RPM	60.11 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_676 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_676 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_676 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_854

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004651	1 retrocopy	retro_btau_1707,
Canis familiaris	ENSCAFG00000019677	4 retrocopies	retro_cfam_1267, retro_cfam_2209, retro_cfam_447, retro_cfam_71,
Canis familiaris	ENSCAFG00000023628	7 retrocopies	retro_cfam_117, retro_cfam_1645, retro_cfam_37, retro_cfam_676 , retro_cfam_69, retro_cfam_832, retro_cfam_96,
Cavia porcellus	ENSCPOG00000008413	1 retrocopy	retro_cpor_599,
Echinops telfairi	ENSETEG00000005563	4 retrocopies	retro_etel_242, retro_etel_547, retro_etel_71, retro_etel_803,
Gorilla gorilla	ENSGGOG00000016526	1 retrocopy	retro_ggor_71,
Monodelphis domestica	ENSMODG00000028492	1 retrocopy	retro_mdom_503,
Mustela putorius furo	ENSMPUG00000015559	5 retrocopies	retro_mputfur_1093, retro_mputfur_1357, retro_mputfur_442, retro_mputfur_667, retro_mputfur_997,
Mus musculus	ENSMUSG00000091228	3 retrocopies	retro_mmus_2712, retro_mmus_3081, retro_mmus_581,
Nomascus leucogenys	ENSNLEG00000007919	2 retrocopies	retro_nleu_1029, retro_nleu_1030,
Oryctolagus cuniculus	ENSOCUG00000022135	1 retrocopy	retro_ocun_1728,
Pan troglodytes	ENSPTRG00000009415	1 retrocopy	retro_ptro_91,
Rattus norvegicus	ENSRNOG00000002693	3 retrocopies	retro_rnor_1198, retro_rnor_1600, retro_rnor_704,