RetrogeneDB ID: retro_fcat_494

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A3:91931708..91932693(-)
• Located in intron of: None

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_494
ATGCCGCACCCATCCCCCCAAACTCAGCCCTCCAACCCTAGTAACTCCCAAGTCTTTTCTGAGGTGGATGTTGGAGGGGA
ACAAGTTGGTTGAATTGTCTTAGAATTGCTTGCAGATATTGTACCCAAAACTGCAGAAAAATTTTGTGCATGTGTACAGG
AGACAAAGGTATTGGACCCACCACTGGGAAACCTCTCCATTTTGAAGGATGCCCTTTCCATCAGATTATTAAGAAATTTA
TGATTCAGGGTGGAGACTTCTCAAATCAAAATGTGACAGGTCGAGAAAGTATTTACGGTGAAAAATTTGAGGATGAAAAT
TTTTATTATAAGCATGATCAGGAAGATTTATCGAGCATGGCAAATGCAGGTTGCAAATACAAATGGTTCTCAGTTCTTTA
TCACAACAGTTTCCCTCTCCTCATTTGGATGGGAAACATGTGATACTTGGCCAAGTAATTAAAGGAATGGGTGTGGCAAG
GATACTGGAAAATGTAGAAGTGAAAGGTGTAAAACCTGCCAAATTGTGTGTTATTGCAGAATGCAAAGAATTGAAGGAAG
GGGATGATTGGAGCATATCTCCAAAAGATGGTTCTGATGACAGTCATCCAGGTTTCCCTGAGGATGCAGATATAGATTTA
AAAGATATAGATAAAATGTTACTAATAACAGAAGACTTAAAAATATTGGAAATACTTTTCTTCAAATCCCAGAACTGGGA
GATGGCCATTAAAAAAATATATGAAAGTTTTAAGATATGTGGAAGGTTCAAAGACTTATTGAGAAAGCAGATAGATTGAA
GCTGCACCGACAGCTTTAAGCTGCGAGCTGAATATTGGTGCTTGTAAACTGGAGATGTCAAGTTGGCAGGGAGCAATTGG
CAGTTGTGTGGAGGCTCTTGAAATAGACCCATCAAATACCAAATCATGGTACTATAGAGCTCAGGGATGGCAAGGATTAA
AAGAATAGATCAAGCATTGGCTGAC

Alignment

ORF - retro_fcat_494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.14 %
• Parental protein coverage: 88.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MSHPSPQTKPSNPSNPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRA-LCTGEKGIGPTTGKPLHFK
          M.HPSPQT.PSNPSN..VF..VD.GGE.VG.IVLEL.ADIVPKTAE.F.A..CTG.KGIGPTTGKPLHF.
Retrocopy MPHPSPQTQPSNPSNSQVFSEVDVGGEQVG*IVLELLADIVPKTAEKFCA<MCTGDKGIGPTTGKPLHFE

Parental  GCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFYYKHDQEGLLSMANAGC-NTNGSQFFITTV-
          GCPFH.IIKKFMIQGGDFSNQN.TG.ESIYGEKFEDENFYYKHDQE.L.SMANAGC.NTNGSQFFITTV.
Retrocopy GCPFHQIIKKFMIQGGDFSNQNVTGRESIYGEKFEDENFYYKHDQEDLSSMANAGC>NTNGSQFFITTV>

Parental  PTPHLDGKHVVFGQVIKGMGVARILENVEVKGEKPAKLCVIAECGELKEGDDWGIFPKDGSGDSHPDFPE
          P.PHLDGKHV..GQVIKGMGVARILENVEVKG.KPAKLCVIAEC.ELKEGDDW.I.PKDGS.DSHP.FPE
Retrocopy PSPHLDGKHVILGQVIKGMGVARILENVEVKGVKPAKLCVIAECKELKEGDDWSISPKDGSDDSHPGFPE

Parental  DADIDLKDVDKILLITED-LKNIGNT-FFKSQNWEMAI-KKYTKVLRYVEGSKAVIEKADRLKLQPIALS
          DADIDLKD.DK.LLITED.LKNIGNT.FFKSQNWEMAI.KKY.KVLRYVEGSK...E........P.ALS
Retrocopy DADIDLKDIDKMLLITED<LKNIGNT>FFKSQNWEMAI>KKYMKVLRYVEGSKTY*E-SR*IEAAPTALS

Parental  CVLNIGACKLKMSNWQGAIDSCLEALEIDPSNTKALYRRAQGWQGLKE-YDQALAD
          C.LNIGACKL.MS.WQGAI.SC.EALEIDPSNTK..Y.RAQGWQGLKE..DQALAD
Retrocopy CELNIGACKLEMSSWQGAIGSCVEALEIDPSNTKSWYYRAQGWQGLKE<IDQALAD

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	0.00 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_494 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_494 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,