RetrogeneDB ID: retro_cfam_496

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:52997450..52997805(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAC1
• Ensembl ID: ENSCAFG00000015716
• Aliases: None
• Description: ras-related C3 botulinum toxin substrate 1 precursor [Source:RefSeq peptide;Acc:NP_001003274]

Sequence

>retro_cfam_496
CTTTTAACTGATGTATTCTTAATTTGTTTTTCTCTTGTGACTCCTGCAACTTTTGAAAATGTTCAAGGAAAGTAATACCC
TAAGTGTTACCACCACTGTCCCAGTACCCCCATCATCCTGGTGAGGGCTAAACTTGATCTCAGATGAAAAAGACATGATT
GAAAAACTGAAGGAGAAAAAGTTGACTCCTATCACCTACCTACAGGGTTTGGTGATGGCTAAGATCACTGCTGTAAAATA
TCTGGAATGCTCAACTCTCAAACAGCAAAGCCTCAAGACAGTGTTTGATGAAGCTAATTGAGCAGTTCTCTGCTCCGTTC
CCATCAAGAAGAGGAAGAGAAAATTCCTGCTGTTG

Alignment

ORF - retro_cfam_496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 56.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LIADVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILV-GTKLDLRDDKDTIEKLKEKKLTPITYPQ
          L..DVFLICFSLV.PA.FENV..K.YP...HHCP.TPIILV.G..L...D.KD.IEKLKEKKLTPITY.Q
Retrocopy LLTDVFLICFSLVTPATFENVQGK*YPKCYHHCPSTPIILV>GLNL-ISDEKDMIEKLKEKKLTPITYLQ

Parental  GLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLCPPPVKKRKRKCLLL
          GL.MAK.I.AVKYLECS.L.Q..LKTVFDEA..AVLC..P.KKRKRK.LLL
Retrocopy GLVMAK-ITAVKYLECSTLKQQSLKTVFDEAN*AVLCSVPIKKRKRKFLLL

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	90.00 RPM
SRP017611_brain	0.00 RPM	97.41 RPM
SRP017611_kidney	0.00 RPM	47.02 RPM
SRP017611_liver	0.00 RPM	28.79 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_496 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_496 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_496 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009233	2 retrocopies	retro_btau_1601, retro_btau_332,
Canis familiaris	ENSCAFG00000014707	5 retrocopies	retro_cfam_1587, retro_cfam_1970, retro_cfam_2189, retro_cfam_88, retro_cfam_89,
Canis familiaris	ENSCAFG00000015716	1 retrocopy	retro_cfam_496 ,
Gorilla gorilla	ENSGGOG00000026733	2 retrocopies	retro_ggor_2110, retro_ggor_217,
Macaca mulatta	ENSMMUG00000021075	4 retrocopies	retro_mmul_1310, retro_mmul_1964, retro_mmul_2642, retro_mmul_721,
Oryctolagus cuniculus	ENSOCUG00000009956	1 retrocopy	retro_ocun_305,
Pan troglodytes	ENSPTRG00000018910	4 retrocopies	retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Xenopus tropicalis	ENSXETG00000027593	1 retrocopy	retro_xtro_1,