RetrogeneDB ID: retro_cfam_2179

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:70497166..70497500(-)
• Located in intron of: ENSCAFG00000017479

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDDC2
• Ensembl ID: ENSCAFG00000001030
• Aliases: None
• Description: HD domain containing 2 [Source:HGNC Symbol;Acc:21078]

Sequence

>retro_cfam_2179
GTTCCAAAAGATGAGCATCTTGAAAAATACCAGAAGCTATGAAGCAGCTAACCCAGCTCCTTCCAGAGGATCTCAGAAAG
GAACTTTATGAAATTCGGGAAAAGTATTAGACCTAACCTAATGCAGAAGCCAAATTTGTGAAGCAGCTGGACCAATGTGA
GATGATTCTTTAGGCATCTGAGTATGAGGACCTTCAGAACAAACCTGGGAAGCTGCAGGGCTTCTATAATTCCATAGCAG
GAAAATTTAGTCACGCTGATTGGTCCAACTTGTTTCTTAACTTGAGGCAGAAAGAAACACTAACATAGCTGCCACCACCA
GTGAGCCATGTTCT

Alignment

ORF - retro_cfam_2179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.54 %
• Parental protein coverage: 56. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IPKEEKHRREE-EAMKQLSQLLPEDLRKELYELWEEYENQSSAEAKFVKQLDQCEMILQASEYEDAENKP
          .PK.E.......EAMKQL.QLLPEDLRKELYE..E.Y.....AEAKFVKQLDQCEMIL.ASEYED..NKP
Retrocopy VPKDEHLEKYQ<EAMKQLTQLLPEDLRKELYEIREKY*T*PNAEAKFVKQLDQCEMIL*ASEYEDLQNKP

Parental  GRLQDFFDSTAGKFSHPE-IVQLVSELEAERNASIAAAAREPSS
          G.LQ.F..S.AGKFSH....VQLVS.LEAERN..IAA...EP.S
Retrocopy GKLQGFYNSIAGKFSHAD<LVQLVS*LEAERNTNIAATTSEPCS

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	16.88 RPM
SRP017611_brain	0.00 RPM	31.12 RPM
SRP017611_kidney	0.00 RPM	29.32 RPM
SRP017611_liver	0.00 RPM	7.11 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2179 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2179 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2179 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009635	1 retrocopy	retro_amel_1399,
Canis familiaris	ENSCAFG00000001030	1 retrocopy	retro_cfam_2179 ,
Microcebus murinus	ENSMICG00000014059	1 retrocopy	retro_mmur_549,
Tupaia belangeri	ENSTBEG00000011826	1 retrocopy	retro_tbel_4277,
Tursiops truncatus	ENSTTRG00000002258	1 retrocopy	retro_ttru_1086,