RetrogeneDB ID: retro_cfam_575

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:43171238..43171515(-)
• Located in intron of: ENSCAFG00000001889

Retrocopy information

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

Parental gene information

• Parental gene symbol: DYNLRB2
• Ensembl ID: ENSCAFG00000020024
• Aliases: None
• Description: dynein, light chain, roadblock-type 2 [Source:HGNC Symbol;Acc:15467]

Sequence

>retro_cfam_575
GCAGAGGTGGAGGAAACCCTAAAGAGGATCCGGAGCCATAAGGGGTCATTGGAACTATGGTTGTAAATGCAGAAGGCATC
CTTATTCGAACGTTGGACAACTCAACAACGGTTCAATATGCAGGTCTTCTTCATCAGCTGATAATGAAAGCCAAGAGCAC
AGTACGTGACATTGATCCTCAGAACGACCTCACTTTTCTTAGGATCAGATCAAAGAAACATGAAATCATGGTAGCCCCAA
AGAATATCTTTTGATTGTCATTCAGAACCCATGTGAA

Alignment

ORF - retro_cfam_575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.6 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AEVEETLKRIQSHKG-VIGTMVVNAEGIPIRTTLDNSTTVQYAGLLHQLTMKAKSTVRDIDPQNDLTFLR
          AEVEETLKRI.SHKG.VIGTMVVNAEGI.IRT.LDNSTTVQYAGLLHQL.MKAKSTVRDIDPQNDLTFLR
Retrocopy AEVEETLKRIRSHKG<VIGTMVVNAEGILIRT-LDNSTTVQYAGLLHQLIMKAKSTVRDIDPQNDLTFLR

Parental  IRSKKHEIMVAPDKEY-LLIVIQNPCE
          IRSKKHEIMVAP.....L...IQNPCE
Retrocopy IRSKKHEIMVAPKNIF<LIV-IQNPCE

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	0.42 RPM	2.23 RPM
SRP017611_brain	0.00 RPM	2.86 RPM
SRP017611_kidney	0.40 RPM	12.94 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_575 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_575 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_575 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007547	6 retrocopies	retro_cfam_1161, retro_cfam_1294, retro_cfam_1577, retro_cfam_1601, retro_cfam_1782, retro_cfam_930,
Canis familiaris	ENSCAFG00000020024	1 retrocopy	retro_cfam_575 ,
Erinaceus europaeus	ENSEEUG00000013344	2 retrocopies	retro_eeur_134, retro_eeur_552,
Sarcophilus harrisii	ENSSHAG00000002755	1 retrocopy	retro_shar_421,