RetrogeneDB ID: retro_fcat_270

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:148847863..148848521(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAFAH1B2
• Ensembl ID: ENSFCAG00000029945
• Aliases: None
• Description: platelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa) [Source:HGNC Symbol;Acc:8575]

Sequence

>retro_fcat_270
ATGAGCCAAGGAGACTCAAACCCAGAAGCTATTCCACATAGAGCAGAAGACATTTAAGGGGATGACAGATGGATGTCTCG
GCACAACGGATTTGTCCTGGACTGTAAAGACAGTGAACCTGTTGTATTGCTTGTGGGGGACTTCATGGTGCAGTTAATGC
AGCAGTAACAATATGGCATTTCCCCCCACTTCATGCACTGAATTTTGGAATTGGCGGAGATACAATAAGAAATGTTTTAT
GAAGGTTAAAGAATGAAGAACTGGAGAATATTAAACCAAAGGTCATTGTTGTCTGGGAAGAAACAAACAACCAAGAAAAT
ATGGCAGAAGTGGCAGGGGGAATTGAGACCATCATACAATCTATCAAAACAAGGAAGCTTCGGACTAAAATCATTGCACT
GGGTTTGTTACTTCTAGGTGAGAAGCCCCACCCTTTGAGGCAAAAAACACAAGGGTGAACCAGCAACTTAAGGTTTCCCT
GCCTAAGCTTGCCAATGTTCAACTCTTAGGTACTGATGGGAGCTTCATGCATTTGGATTGTGCCATCTCCTGCCACGACG
TGTTTTATCTTCTGCATCTCACAGGAGGGGGCTATGCAGAGTTCTGCAAACCACTGCATGGACTGATCATGCAATTGTTA
GAGGACACCCCAGGAGAA

Alignment

ORF - retro_fcat_270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76. %
• Parental protein coverage: 97.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSQGDSNPAAIPHAAEDIQGDDRWMSQHNRFVLDCKDKEPDVLFVGDSMVQLMQQYE-IWRELFSPLHAL
          MSQGDSNP.AIPH.AEDI.GDDRWMS.HN.FVLDCKD.EP.VL.VGD.MVQLMQQ...IW...F.PLHAL
Retrocopy MSQGDSNPEAIPHRAEDI*GDDRWMSRHNGFVLDCKDSEPVVLLVGDFMVQLMQQ*Q<IWH--FPPLHAL

Parental  NFGIGGDTTRHVLWRLKNGELENIKPKVIVVWVGTNNHENTAEEVAGGIEAIVQLINTRQPQAKIIVLGL
          NFGIGGDT.R.VL.RLKN.ELENIKPKVIVVW..TNN.EN.AE.VAGGIE.I.Q.I.TR....KII.LGL
Retrocopy NFGIGGDTIRNVL*RLKNEELENIKPKVIVVWEETNNQENMAE-VAGGIETIIQSIKTRKLRTKIIALGL

Parental  LPRGEKPNPLRQK-NAKVNQLLKVSLPKLANVQLLDTDGGFVHSDGAISCHDMFDFLHLTGGGYAKICKP
          L..GEKP.PLRQK.N..VNQ.LKVSLPKLANVQLL.TDG.F.H.D.AISCHD.F..LHLTGGGYA..CKP
Retrocopy LLLGEKPHPLRQK<NTRVNQQLKVSLPKLANVQLLGTDGSFMHLDCAISCHDVFYLLHLTGGGYAEFCKP

Parental  LHELIMQLLEETPEE
          LH.LIMQLLE.TP.E
Retrocopy LHGLIMQLLEDTPGE

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	124.30 RPM
SRP017611_kidney	0.00 RPM	38.54 RPM
SRP017611_liver	0.00 RPM	21.73 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_270 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_270 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.

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008628	2 retrocopies	retro_amel_1145, retro_amel_818,
Canis familiaris	ENSCAFG00000013226	1 retrocopy	retro_cfam_1335,
Callithrix jacchus	ENSCJAG00000012698	1 retrocopy	retro_cjac_3325,
Dipodomys ordii	ENSDORG00000011274	1 retrocopy	retro_dord_560,
Felis catus	ENSFCAG00000029945	1 retrocopy	retro_fcat_270 ,
Homo sapiens	ENSG00000168092	2 retrocopies	retro_hsap_1148, retro_hsap_4661,
Gorilla gorilla	ENSGGOG00000028197	2 retrocopies	retro_ggor_2893, retro_ggor_893,
Macaca mulatta	ENSMMUG00000002050	2 retrocopies	retro_mmul_2481, retro_mmul_892,
Mustela putorius furo	ENSMPUG00000004246	1 retrocopy	retro_mputfur_898,
Nomascus leucogenys	ENSNLEG00000007337	2 retrocopies	retro_nleu_1096, retro_nleu_946,
Pongo abelii	ENSPPYG00000003907	2 retrocopies	retro_pabe_3621, retro_pabe_953,
Pan troglodytes	ENSPTRG00000004318	2 retrocopies	retro_ptro_3097, retro_ptro_782,
Rattus norvegicus	ENSRNOG00000018032	1 retrocopy	retro_rnor_2585,
Sarcophilus harrisii	ENSSHAG00000011403	1 retrocopy	retro_shar_617,