RetrogeneDB ID: retro_cfam_2075

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:47261472..47262116(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRC2
• Ensembl ID: ENSCAFG00000017756
• Aliases: None
• Description: ubiquinol-cytochrome c reductase core protein II [Source:HGNC Symbol;Acc:12586]

Sequence

>retro_cfam_2075
ATTGACAAAGCTGTGGCTTTTTAGAACCCACAGGCTCATGTCCTTGAAAATTTGCATGCTGCAGCTTACCGAAATTCCTT
GGCTAATTCCCTATATGTCCTGACTACAGGATTGGAAAAGTGACACCAGATGAGTTGCATTACTATGTTCAGAACCATTT
CACAAGTGCAAGAATGGCTTTTATTGGACTTGGTGTGAGTCACCCTGTTCTAAAGCAAGTTGTGGAACAGTTTCTCAACA
TGAGGGGCAGGCTTGGTTTACCTGGTGCAAAGGCCAGATACCGTGGAGGTGAAATCCGAGAGCAGAATGGAGACAGTCTT
GTTCATGCAGCTCTTGTAGCAGAAGGTGCTGCTACAGGAAGTACAGAAGCAAATGCATTTAGTGTTCTCCAGTATGTCCT
TGGTGCTGGACCACATGTCAAGAGGGGCAGCAATCCCACCAGTTCCCTATACCAGGCTGTTGCCAAGGGAGTTCACCAGC
CATTTGATGTTTCTGCTTTTAATGCCAGTTACTCTGATTCTGGACTCTTTGGGATTTACACCATCTCACAGGCTGCTGCA
GCTGGAGATGTTATCAAGGCTGCCTATAATCAAGTAAAAACAGTTGCTCAAGGAAACCTTTCCAGTGTAGATGTCCAAGT
TGCC

Alignment

ORF - retro_cfam_2075 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.3 %
• Parental protein coverage: 56.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDKAVAFQNPQAHVLENLHAAAYRNALANSLY-CPDYRIGKVTPDELHYYVQNHFTSARMALIGLGVGHP
          IDKAVAF.NPQAHVLENLHAAAYRN.LANSLY.CPDYRIGKVTPDELHYYVQNHFTSARMA.IGLGV.HP
Retrocopy IDKAVAF*NPQAHVLENLHAAAYRNSLANSLY<CPDYRIGKVTPDELHYYVQNHFTSARMAFIGLGVSHP

Parental  VLKQVAEQFLNMRGGLGLPGAKARYRGGEIREQNGDSLVHAALVAEGAAIGSTEANAFSVLQYVLGAGPH
          VLKQV.EQFLNMRG.LGLPGAKARYRGGEIREQNGDSLVHAALVAEGAA.GSTEANAFSVLQYVLGAGPH
Retrocopy VLKQVVEQFLNMRGRLGLPGAKARYRGGEIREQNGDSLVHAALVAEGAATGSTEANAFSVLQYVLGAGPH

Parental  VKRGSNPTSSLYQAVAKGVHQPFDVSAFNASYSDSGLFGIYTISQAAAAGDVIKAAYNQVKTVAQGNLSS
          VKRGSNPTSSLYQAVAKGVHQPFDVSAFNASYSDSGLFGIYTISQAAAAGDVIKAAYNQVKTVAQGNLSS
Retrocopy VKRGSNPTSSLYQAVAKGVHQPFDVSAFNASYSDSGLFGIYTISQAAAAGDVIKAAYNQVKTVAQGNLSS

Parental  VDVQVA
          VDVQVA
Retrocopy VDVQVA

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	1.34 RPM	62.07 RPM
SRP017611_brain	0.56 RPM	82.25 RPM
SRP017611_kidney	4.16 RPM	217.46 RPM
SRP017611_liver	0.94 RPM	68.89 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2075 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2075 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2075 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021651	2 retrocopies	retro_btau_1008, retro_btau_1668,
Canis familiaris	ENSCAFG00000017756	1 retrocopy	retro_cfam_2075 ,
Callithrix jacchus	ENSCJAG00000009116	1 retrocopy	retro_cjac_222,
Echinops telfairi	ENSETEG00000001084	1 retrocopy	retro_etel_2087,
Homo sapiens	ENSG00000140740	1 retrocopy	retro_hsap_2785,
Gorilla gorilla	ENSGGOG00000015379	1 retrocopy	retro_ggor_1941,
Myotis lucifugus	ENSMLUG00000003345	2 retrocopies	retro_mluc_1391, retro_mluc_770,
Macaca mulatta	ENSMMUG00000018287	2 retrocopies	retro_mmul_1442, retro_mmul_683,
Monodelphis domestica	ENSMODG00000007645	1 retrocopy	retro_mdom_327,
Mustela putorius furo	ENSMPUG00000016849	1 retrocopy	retro_mputfur_1042,
Nomascus leucogenys	ENSNLEG00000012185	1 retrocopy	retro_nleu_685,
Oryctolagus cuniculus	ENSOCUG00000003891	2 retrocopies	retro_ocun_604, retro_ocun_739,
Otolemur garnettii	ENSOGAG00000005478	4 retrocopies	retro_ogar_1113, retro_ogar_112, retro_ogar_1934, retro_ogar_82,
Ochotona princeps	ENSOPRG00000000419	1 retrocopy	retro_opri_455,
Pongo abelii	ENSPPYG00000007174	1 retrocopy	retro_pabe_2232,
Pan troglodytes	ENSPTRG00000007871	1 retrocopy	retro_ptro_1886,
Sorex araneus	ENSSARG00000010670	1 retrocopy	retro_sara_231,
Tupaia belangeri	ENSTBEG00000010785	1 retrocopy	retro_tbel_3988,