RetrogeneDB ID: retro_cfam_2030

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: JH373319.1:12048..12673(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000024953
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STARD5
• Ensembl ID: ENSCAFG00000013792
• Aliases: None
• Description: StAR-related lipid transfer (START) domain containing 5 [Source:HGNC Symbol;Acc:18065]

Sequence

>retro_cfam_2030
GTGGCCGCGCAGATGAGCGACGCGGTGGCGGAGAAGGTGCTCCGGTCCGGCGGGAGGAGTCAGGATGGAAGATTTGCCGG
GAAGGCAATGGAGTTTCAGTTTCCCGGAGGCCATCTGTGGAGTTTCCAGGGAACCTGTGCCGGGGAGAAGGCATTGTGAA
CTCGACACCAGACAGAGTGTGGGGCTGCATGAAGCCGCTTGCTGGGACCCTGCGAGACAAGTGGGATGAGAATGTGAGCA
GCTTTGAAATTATCGAAAGCATCACTGATATGCTGTGCGTGAGCAGAACCGCCACCCCCTCGGCTGCCACGAAGCTCATT
TCCCCCAGGGACTTTGTGGACTTGGTGCTAGTCAAGAAGTGTGAGGACGGGATGCTCAGTTCCAATGCTGTCCACGTAGA
ACACCTGTTATGTCCTCTGAAGCCAGGTTACGTGAGAGGGTTTAACCACCCTTGTGGGTGCTTCTGTGAGCCTCTGCCAG
GGGAGCCCAACAAGACCAAGCTGGTCACGTTCTTCCAGACTGACCTCAGTGGCTACCTCCGCCGAGTGTGGTGGACTCCT
TCTTCCCCCGCAGCATGGCCGGTCTCTACACCAACCTGGAGAAAGCAGTGAAGAGGCTTTATGAC

Alignment

ORF - retro_cfam_2030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91. %
• Parental protein coverage: 98.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAAQMSEAVAEKVLR-YRRDESGWKICREGNGVSVSWRPSMEFPGNLYRGEGIVNSTPEKVWGCIKPLAG
          VAAQMS.AVAEKVLR..RR.ESGWKICREGNGVSVS.RPS.EFPGNL.RGEGIVNSTP..VWGC.KPLAG
Retrocopy VAAQMSDAVAEKVLR<VRREESGWKICREGNGVSVSRRPSVEFPGNLCRGEGIVNSTPDRVWGCMKPLAG

Parental  TLRDKWDENVSSFEIIESITDMLCVSRTATPSAAMKLISPRDFVDLVLVKKYEDGTLSSNAVNVEHPLCP
          TLRDKWDENVSSFEIIESITDMLCVSRTATPSAA.KLISPRDFVDLVLVKK.EDG.LSSNAV.VEH.LCP
Retrocopy TLRDKWDENVSSFEIIESITDMLCVSRTATPSAATKLISPRDFVDLVLVKKCEDGMLSSNAVHVEHLLCP

Parental  PKPGYVRGFNHPCGCFCEPLPGEPNKTKLVTFFQTDLSGYL-PQSVVDSFFPRSMAGFYTNLEKAVKRLY
          .KPGYVRGFNHPCGCFCEPLPGEPNKTKLVTFFQTDLSGYL.P.SVVDSFFPRSMAG.YTNLEKAVKRLY
Retrocopy LKPGYVRGFNHPCGCFCEPLPGEPNKTKLVTFFQTDLSGYL<PPSVVDSFFPRSMAGLYTNLEKAVKRLY

Parental  D
          D
Retrocopy D

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	2.73 RPM	3.36 RPM
SRP017611_brain	17.55 RPM	5.72 RPM
SRP017611_kidney	0.46 RPM	3.96 RPM
SRP017611_liver	29.30 RPM	55.04 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2030 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2030 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2030 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013792	1 retrocopy	retro_cfam_2030 ,
Canis familiaris	ENSCAFG00000030762	1 retrocopy	retro_cfam_902,