RetrogeneDB ID: retro_fcat_1307

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:135965175..135965860(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX18
• Ensembl ID: ENSFCAG00000013950
• Aliases: None
• Description: COX18 cytochrome C oxidase assembly factor [Source:HGNC Symbol;Acc:26801]

Sequence

>retro_fcat_1307
CACTACGTCCTGGCCAAGGTGGAAAATTTGCAGCCAGAAATAAAAAGCATTGCAAGGCATCTCAACCAAGAAGGTGCAGT
TAGTGCAGATCAGTTGAGGTGGTCCAAAAGAGTTGCCAGGCCAACTTACCTAAAGAATACGGGGGGCTTGTTTCAAGAGC
TATATGTTAGGGATAACTGCCACCCTCTCAAAGCCTCTGTGTTGGTCTGGATTCGGTTTCCAATGTGGATCTTCATGTCT
GTTGCTCTTTGGAATTTTAGCACAGGGGCAACACATTCAGATGTAGGTTTTTCTATTCAGGAACAGTTACCTACTAGTAG
GGTCCTGTGGTTTCCTGACCTCACTGCACTGGATTCCTCTTGGATTCTGCTTATCTCTGTTGGTGTCATCAGTTTATTAA
TAGTGGAGATTTTTGCTCTGCAAAAAATTGGAATGACTCCTTTTCAGATGTATATTACGTGCTTTGTTCGTGTGGTATCA
GTGTTGATGATTCCAATTGCTGCAACAGTACCTTCATCAATTGTCCTCTACTGCTTATGTTCCAGATTCATGGGCCTTTC
ACAGAATTTGTTGTTGCATTCTCCTAGGTTTTTGCCAACTTTGCCAAATACCGTTGACCACGTCAGATTCAGACACGCCT
TGTAAGGACCTCTTTGCCACCTTTTATGCTAAGTTTATTTCAAGA

Alignment

ORF - retro_fcat_1307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.6 %
• Parental protein coverage: 67.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HYILAKVENLQPEIKNIARHLNQEIAIRANQLKWSKRAARLTYLKNMRRLVSELYVRDNCHPFKATVLVW
          HY.LAKVENLQPEIK.IARHLNQE.A..A.QL.WSKR.AR.TYLKN...L..ELYVRDNCHP.KA.VLVW
Retrocopy HYVLAKVENLQPEIKSIARHLNQEGAVSADQLRWSKRVARPTYLKNTGGLFQELYVRDNCHPLKASVLVW

Parental  IQFPMWIFMSIALRNFSTGATHSEAGFSVQEQLANDGILWFRDLTALDSTWILPISVGVTNLLIVEIFAL
          I.FPMWIFMS.AL.NFSTGATHS..GFS.QEQL.....LWF.DLTALDS.WIL.ISVGV..LLIVEIFAL
Retrocopy IRFPMWIFMSVALWNFSTGATHSDVGFSIQEQLPTSRVLWFPDLTALDSSWILLISVGVISLLIVEIFAL

Parental  QKTGMSRFQTYITYFVRAVSVLMIPVAATVPSSIVLYWLCSSFMGLSQNLLLRSPRFR-RLCRIPLTKSD
          QK.GM..FQ.YIT.FVR.VSVLMIP.AATVPSSIVLY.LCS.FMGLSQNLLL.SPRF...LC.IPLT.SD
Retrocopy QKIGMTPFQMYITCFVRVVSVLMIPIAATVPSSIVLYCLCSRFMGLSQNLLLHSPRFL>QLCQIPLTTSD

Parental  SDTPYKDLFAAFYAKFISR
          SDTP.KDLFA.FYAKFISR
Retrocopy SDTPCKDLFATFYAKFISR

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
SRP017611_brain	0.00 RPM	5.97 RPM
SRP017611_kidney	0.00 RPM	6.90 RPM
SRP017611_liver	0.00 RPM	2.02 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1307 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1307 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000013950	1 retrocopy	retro_fcat_1307 ,