RetrogeneDB ID: retro_fcat_986

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:105810702..105811039(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf57
• Ensembl ID: ENSFCAG00000026799
• Aliases: None
• Description: chromosome 6 open reading frame 57 [Source:HGNC Symbol;Acc:20957]

Sequence

>retro_fcat_986
GCCCAAGTTGGTACCATGATTGTATCAGGGGTAGCTGGGTGGCCTGGCTGCATCCCGGCCACAGTGTGAAGAGTGGCAAG
ATCACCCCTTCTGAGTCATCCTGTGAGGAAAATGAGTTCTCAAGGAGAAAAAATCCAAAGCCATTAAATGATCTCTAAAG
AAGCCAAAGTTACCAGAAGGTTGTTTTGATGCACCAGAAGATTCTCATTTAGAGAAAGAACCAGCGGCAAAATTTCTGGA
TGATGTTAATCCTGTTACCAAAGACAAAGGTGGCCCCAGGGCCCCAGAACCTAACCAATATGGAAACTGGAGATGAAAAG
TACACTGTATTGATTTT

Alignment

ORF - retro_fcat_986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.26 %
• Parental protein coverage: 98.25 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGVGNMTVTRLARLLGYIPATAWRAARSPLVCCSVRKMSSQGEK-SKPIKQSHKKPKLPEGRFDAPEDPN
          A.VG.M.V...A...G.IPAT..R.ARSPL....VRKMSSQGEK.SK.IK.S.KKPKLPEG.FDAPED..
Retrocopy AQVGTMIVSGVAGWPGCIPATV*RVARSPLLSHPVRKMSSQGEK>SKAIK*SLKKPKLPEGCFDAPEDSH

Parental  LEKEPLTKFPDDINPVTKEKGGPRGPEPTRYGDWERKGRCIDF
          LEKEP..KF.DD.NPVTK.KGGPR.PEP..YG.W..K..CIDF
Retrocopy LEKEPAAKFLDDVNPVTKDKGGPRAPEPNQYGNWR*KVHCIDF

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	23.41 RPM
SRP017611_kidney	0.00 RPM	11.75 RPM
SRP017611_liver	0.00 RPM	11.83 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_986 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_986 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002602	2 retrocopies	retro_cfam_268, retro_cfam_657,
Choloepus hoffmanni	ENSCHOG00000011410	6 retrocopies	retro_chof_176, retro_chof_1854, retro_chof_252, retro_chof_465, retro_chof_694, retro_chof_966,
Erinaceus europaeus	ENSEEUG00000011260	1 retrocopy	retro_eeur_539,
Echinops telfairi	ENSETEG00000011154	1 retrocopy	retro_etel_1362,
Felis catus	ENSFCAG00000026799	1 retrocopy	retro_fcat_986 ,
Rattus norvegicus	ENSRNOG00000028087	1 retrocopy	retro_rnor_1514,
Tupaia belangeri	ENSTBEG00000004344	2 retrocopies	retro_tbel_3788, retro_tbel_4408,
Tarsius syrichta	ENSTSYG00000001769	1 retrocopy	retro_tsyr_67,