RetrogeneDB ID: retro_cfam_501

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:65407738..65408051(+)
• Located in intron of: ENSCAFG00000003778

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB22A
• Ensembl ID: ENSCAFG00000012101
• Aliases: None
• Description: Canis lupus familiaris RAB22A, member RAS oncogene family (RAB22A), mRNA. [Source:RefSeq mRNA;Acc:NM_001003208]

Sequence

>retro_cfam_501
ACATATTTTGTCTAGTACCAAAATGAGCATGTAAATTCCTAATCTGGGACATAACTGCACAAGAATGATTTTCTGCTTTA
CCAGAATGTACTATTAGTTACCTTCAGCTATAATAATTAGTGATACCAAAAAGAGGAAATATTTTCAACATTAAGGGATC
GATTAAGAGATCTTTAACAGCAAGGACTATCTAATTTTGTCGTTGACATTGCAGGAAATAAGTGTGATATTATCATAAAA
GGGAAATCATGGAGAGAGATGCTAAGGACTCCACTGACTCATCCATACAGTTTTTATAGAGAGCAGTGCAAAA

Alignment

ORF - retro_cfam_501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.25 %
• Parental protein coverage: 70.39 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  TKTVQYQNE-LHKFLIWDTAGQERFRALAP-MYYRGSAAAIIVYDITK-EETFSTLKNWVKELRQHGPPN
          T..V.YQNE...KFLIWD...QE.F.AL...MYY.....AII..D..K.EE.FSTL......L.Q.G..N
Retrocopy TYFV*YQNE<ACKFLIWDITAQE*FSALPE<MYY*-LPSAIIISDTKK<EEIFSTLRDRLRDL*QQGLSN

Parental  IVVAIAGNKCDLI-DVREVMERDAKDYADS-IHAIFVETSAK
          .VV.IAGNKCD.I...RE.MERDAKD..DS.IH..F.E.SAK
Retrocopy FVVDIAGNKCDII<HKREIMERDAKDSTDS<IHTVFIESSAK

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	13.57 RPM
SRP017611_brain	0.00 RPM	10.72 RPM
SRP017611_kidney	0.00 RPM	9.77 RPM
SRP017611_liver	0.00 RPM	4.64 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_501 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_501 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_501 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012646	1 retrocopy	retro_amel_617,
Canis familiaris	ENSCAFG00000012101	1 retrocopy	retro_cfam_501 ,
Callithrix jacchus	ENSCJAG00000019039	2 retrocopies	retro_cjac_1715, retro_cjac_842,
Microcebus murinus	ENSMICG00000008382	1 retrocopy	retro_mmur_1546,
Oryctolagus cuniculus	ENSOCUG00000004414	1 retrocopy	retro_ocun_554,
Otolemur garnettii	ENSOGAG00000015779	1 retrocopy	retro_ogar_2851,