RetrogeneDB ID: retro_cfam_1091

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:1838915..1839657(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000005665
• Aliases: None
• Description: KRR1 small subunit processome component [Source:UniProtKB/TrEMBL;Acc:E2R869]

Sequence

>retro_cfam_1091
ATGGTGTCCTCCTCCATCAACGGGCTAGCCAGGGCCAATGGGAGAAGTGAATTTCGTCCCAAGCAGCCAAAGCCAGAGAA
CGGAGATGAATCAGAACTCCTCACTGTTCCTGATGGTTGGAAGGAACCGGCTTTTTCTAAAGAGGACAATCCCAGAGGAC
TCTTGGAAGAGAGCAGTTTTGCAACTTTGTTCCCAAAATATAGAGTCTTACTTGGAAGAGTGCTGGCCTTAGGTACAGAA
AGCCTTGAATGAACATCACATTAATGCAACCCTGGACCTGATCGAGGGCAGTATGACTGTTTGTACAACAAAGAAGGCTT
TCGATCCATATATCATAATTAGGGCCAGAGACCTAATAAAACTTTTGGCAAGAAGTGTTTCATTTGAATAGGCAGTACGA
ATTCTTCAGGATGATATTGCATGTGACATCATGAAAATAGGTTCTTTAGTAACAAATAAAGAAAGATTTGTAAAAAGAAG
ACAATATCTCATTGGTCCCAAAGGATCTAGATTAAAGGCTTTGGAACTCTTAACAAATTGTTATATTATGGTTCAGGGAA
ACACGGTTTCAGTCATTGGACCTTTTAGTGGCTTAAAAGAGGTTTGAAAAGTAGTCCTAGATACTATGAAGAATATTCAT
CCAATTTATAACATTAAAACCTTAATGACTAAACGAGAGTTGGCAAAAGATTCTGAATTAAGATCACAAAGTTGGGAAAG
ATTCTTGCCACAGTTCAAGCAC

Alignment

ORF - retro_cfam_1091 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.8 %
• Parental protein coverage: 65.26 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASSFHGLAQANGRSEFRPKQPKPEKRDESELLTVPDGWKEPAFSKEDNPRGLLEESS-FATLFPKY-R
          M..SS..GLA.ANGRSEFRPKQPKPE..DESELLTVPDGWKEPAFSKEDNPRGLLEESS.F....PK...
Retrocopy MVSSSINGLARANGRSEFRPKQPKPENGDESELLTVPDGWKEPAFSKEDNPRGLLEESS<FCNFVPKI<I

Parental  EAYLKECWPLVQKALNEHHVNATLDLIEGSMTVCTTKKTFDPYIIIRARDLIKLLARSVSFEQAVRILQD
          E.YL.ECWP.VQKALNEHH.NATLDLIEGSMTVCTTKK.FDPYIIIRARDLIKLLARSVSFE.AVRILQD
Retrocopy ESYLEECWP*VQKALNEHHINATLDLIEGSMTVCTTKKAFDPYIIIRARDLIKLLARSVSFE*AVRILQD

Parental  DVACDIIKIGSLVRNKERFVKRRQRLIGPKGSTLKALELLTNCYIMVQGNTVSVIGPFSGLKEVRKVVLD
          D.ACDI.KIGSLV.NKERFVKRRQ.LIGPKGS.LKALELLTNCYIMVQGNTVSVIGPFSGLKEV.KVVLD
Retrocopy DIACDIMKIGSLVTNKERFVKRRQYLIGPKGSRLKALELLTNCYIMVQGNTVSVIGPFSGLKEV*KVVLD

Parental  TMKNIHPIYNIKTLMIKRELAKDSELRSQSWERFLPQFKH
          TMKNIHPIYNIKTLM.KRELAKDSELRSQSWERFLPQFKH
Retrocopy TMKNIHPIYNIKTLMTKRELAKDSELRSQSWERFLPQFKH

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	20.62 RPM
SRP017611_brain	0.00 RPM	15.88 RPM
SRP017611_kidney	0.00 RPM	19.68 RPM
SRP017611_liver	0.00 RPM	7.40 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1091 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1091 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1091 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006437	1 retrocopy	retro_amel_1292,
Canis familiaris	ENSCAFG00000005665	1 retrocopy	retro_cfam_1091 ,
Choloepus hoffmanni	ENSCHOG00000009636	5 retrocopies	retro_chof_1030, retro_chof_1826, retro_chof_2438, retro_chof_2452, retro_chof_365,
Monodelphis domestica	ENSMODG00000020451	1 retrocopy	retro_mdom_791,
Tupaia belangeri	ENSTBEG00000008145	5 retrocopies	retro_tbel_1056, retro_tbel_2060, retro_tbel_2911, retro_tbel_2915, retro_tbel_3679,