RetrogeneDB ID: retro_cfam_902

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:49315677..49316248(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STARD4
• Ensembl ID: ENSCAFG00000030762
• Aliases: None
• Description: StAR-related lipid transfer (START) domain containing 4 [Source:HGNC Symbol;Acc:18058]

Sequence

>retro_cfam_902
ATGGAAGGCCTGCCTGATGCTGCTGCTTTTGCAACTAGACTTAAAAACACTCTCATCCAATATCATGGCATCAGAGATGA
TAAGTGGTGAGTTGCCAAGAAAATGAAAGATACAACAATTTGGAGAAAACCTTCAGAAGAATTTAATGGATACCTTTTCA
AAGCCCAGGGTGTTACAGATGACATTGTGAATAGTGTCATAGACCATATACACCCGAGTCCCTGTCGCTTGGATTGGGAC
AGCTTAATGACTTCAATGGATATTTTGGAACACTTTGAAGAGAATTGCTGTGTGATGCGTTACATTACTGCTGGTCAGTT
TAGGAATATAATTTCCCCACAAGAGTTTGTGGGTTTCTCCTACACCATGGGCTACAAAGACGTAGGCTTTTGTCCTGTGG
GCTAAGTGTTGGCTGGAGTGAAAAGAGACCAGGTTTATTCGTGGATTTCACCATCCCTGTGGCTGGTTCTGTGTTCCACG
TAAAGACAATCGCCAGCAGAGTCTCTTGATGGGGCATATTCAGATGGATCTCTGTGGGATGATCCTGCAGTCTGCGGCCG
ACACAGCCATG

Alignment

ORF - retro_cfam_902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.87 %
• Parental protein coverage: 98.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEGLPDAAAFATRLKNTLIQYHSIEDDKWRVAKKVKDVTIWRKPSEEFNGYLFKAQGVIDDIVNSVIDHI
          MEGLPDAAAFATRLKNTLIQYH.I.DDKW.VAKK.KD.TIWRKPSEEFNGYLFKAQGV.DDIVNSVIDHI
Retrocopy MEGLPDAAAFATRLKNTLIQYHGIRDDKW*VAKKMKDTTIWRKPSEEFNGYLFKAQGVTDDIVNSVIDHI

Parental  RPGPYRLDWDSLMTSMDILEHFEENCCVMRYTTAGQLWNIISPREFVDFSYTVDYED-GLLSCG-LSVDW
          .P.P.RLDWDSLMTSMDILEHFEENCCVMRY.TAGQ..NIISP.EFV.FSYT..Y.D.G....G.LSV.W
Retrocopy HPSPCRLDWDSLMTSMDILEHFEENCCVMRYITAGQFRNIISPQEFVGFSYTMGYKDVGFCPVG<LSVGW

Parental  SEQRP-EFIRGFNHPCGWFCVPRKDNPQQSLLTGYIQTDLRGMIPQSAVDTAM
          SE.RP..FIRGF.HPCGWFCVPRKDN.QQSLL.G.IQ.DL.GMI.QSA.DTAM
Retrocopy SEKRP<RFIRGFHHPCGWFCVPRKDNRQQSLLMGHIQMDLCGMILQSAADTAM

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	21.50 RPM
SRP017611_brain	0.00 RPM	25.96 RPM
SRP017611_kidney	0.00 RPM	23.25 RPM
SRP017611_liver	0.00 RPM	11.17 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_902 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_902 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_902 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013792	1 retrocopy	retro_cfam_2030,
Canis familiaris	ENSCAFG00000030762	1 retrocopy	retro_cfam_902 ,
Otolemur garnettii	ENSOGAG00000007595	2 retrocopies	retro_ogar_2798, retro_ogar_929,