RetrogeneDB ID: retro_fcat_559

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:116788228..116788852(+)
• Located in intron of: ENSFCAG00000014486

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPID
• Ensembl ID: ENSFCAG00000028926
• Aliases: None
• Description: peptidylprolyl isomerase D [Source:HGNC Symbol;Acc:9257]

Sequence

>retro_fcat_559
ATGTCACACCCATCCCCCAAAACTAAGCCCTCCAACCCCCAGCAACCCCTGAGTCTTTTTTGACATGGACATCGGAGGGC
AGTGAGTTGGTTGAATTGTCTTAGAATTGTTTGCAGATGTTGTACCCAAAACTGTAGAAAATTTCTGTGCATTGTGTAGA
GGAGAAAAAGGCATTGGACTCACCACCGGAAACCTCTCCATTTCAAGGATGCCCTTTTCATCGATTATTAAGAAATTTAT
GATTCAGGGTAGAGACTTCTCAAAACAAAATGGGACAGGTGGAGAAAATATTGATGGGACAGGTGGAGGATGAAAATTTC
TCTTACAAGCTTAACCAGGACGGTTTATTGAGCACGGCAAATGTGGGCTGCGATACAAATGGTTCTCAGTTCTTATCACA
ACAGATCCCACTCCTCGTTTGGAAGGAAACATGTGGTATTTGGTCAAGTAATTAAAGAAATGGGTGTGGCAAGGATACTG
GGAAATGTAGAAGTGAAAGGTAAAAAAACCTGCCAAATTGTGTGTTACTACAGAATGTGGGGAATTGAAGGAGGGGAATG
ATTGGGACGTATTCCCAATAGATGTTCTGGTGACAGTCATCCAGATTTCCCTGAGGATGTAGAT

Alignment

ORF - retro_fcat_559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.17 %
• Parental protein coverage: 56.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  MSHPSPQTKPSNP-SNPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTG-KPLHF
          MSHPSP.TKPSNP.SNP.VFFD.DIGG..VG.IVLELFAD.VPKT.ENF.ALC.GEKGIG.TTG.KPLHF
Retrocopy MSHPSPKTKPSNP>SNP*VFFDMDIGGQ*VG*IVLELFADVVPKTVENFCALCRGEKGIGLTTG<KPLHF

Parental  K-GCPFHR-IIKKFMIQGGDFSNQNGTGGES-IYGEKFEDENFYYKHDQEGLLSMANAGCNTNGSQFF-I
          K.GCPFHR.IIKKFMIQG.DFS.QNGTGGE....G...EDENF.YK..Q.GLLS.AN.GC.TNGSQF..I
Retrocopy K<GCPFHR<IIKKFMIQGRDFSKQNGTGGEN>LMGQ-VEDENFSYKLNQDGLLSTANVGCDTNGSQFL<I

Parental  TTVPTPHLDG-KHVVFGQVIKGMGVARILENVEVKGEK-PAKLCVIAECGELKEGDDWGIFPKDG-SGDS
          TT.PTP.L.G.KHVVFGQVIK.MGVARIL.NVEVKG.K.PAKLCV..ECGELKEG.DW..FP.D..SGDS
Retrocopy TTDPTPRLEG<KHVVFGQVIKEMGVARILGNVEVKGKK>PAKLCVTTECGELKEGNDWDVFPIDV<SGDS

Parental  HPDFPEDAD
          HPDFPED.D
Retrocopy HPDFPEDVD

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	30.30 RPM
SRP017611_kidney	0.21 RPM	20.51 RPM
SRP017611_liver	0.00 RPM	15.47 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_559 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_559 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 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016680	1 retrocopy	retro_btau_1672,
Choloepus hoffmanni	ENSCHOG00000012069	1 retrocopy	retro_chof_1533,
Callithrix jacchus	ENSCJAG00000001437	2 retrocopies	retro_cjac_2321, retro_cjac_4162,
Cavia porcellus	ENSCPOG00000001046	2 retrocopies	retro_cpor_275, retro_cpor_436,
Echinops telfairi	ENSETEG00000012655	2 retrocopies	retro_etel_10, retro_etel_633,
Felis catus	ENSFCAG00000028926	2 retrocopies	retro_fcat_494, retro_fcat_559 ,
Myotis lucifugus	ENSMLUG00000009317	1 retrocopy	retro_mluc_1667,
Macaca mulatta	ENSMMUG00000017768	2 retrocopies	retro_mmul_281, retro_mmul_348,
Mustela putorius furo	ENSMPUG00000018108	1 retrocopy	retro_mputfur_1415,
Oryctolagus cuniculus	ENSOCUG00000006602	1 retrocopy	retro_ocun_1625,
Otolemur garnettii	ENSOGAG00000003317	2 retrocopies	retro_ogar_2355, retro_ogar_2680,
Pongo abelii	ENSPPYG00000015159	1 retrocopy	retro_pabe_3594,
Rattus norvegicus	ENSRNOG00000027408	1 retrocopy	retro_rnor_188,
Ictidomys tridecemlineatus	ENSSTOG00000001552	1 retrocopy	retro_itri_1422,