RetrogeneDB ID: retro_fcat_2015

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:102745513..102746355(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC1
• Ensembl ID: ENSFCAG00000011310
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 1 [Source:HGNC Symbol;Acc:9547]

Sequence

>retro_fcat_2015
ATAGAGGTGCTCATGGATGACACAGATCCCTTGGTTACAGGGATGAAGGTAGGAAAGTCCCCCCAGGAAACCTATGCTGA
TTTTGGGGGGTTGGACAACCAAATCCAGGAAATTAAGGAATCTGTGGAGCTTCCTCTCAATCATCTTGAATATTATGAAG
AGATGGATATGAAGCCCCAAGGGGTCATTCTAGATGATCTGCCAGGCACAAGCAAAACCTTATTAGCTAAAGCAGTAGCA
AACCAAACCTCAGCCACATTCTTGAGAGTGGTTGACACTGAACTTATCCAGAAGTACCTAGGTGATGGGTCCAAACTCAT
TCAGGAATTGTTTTGAGTTGCAGAAGAACATGCACCATCCATTGTGTTTATTGATGAAATTGATGCCATTGGGACAAAAA
GATAAGACTCAAATTCCAGTCGTGAGAGAGAAATTCAATGAACCATGTTGGAACCATTGAAACAGTTGGATGGATTTGAT
ATAAGGGGTGACATGAAAGTTATCATGGCCGCAAACTGAATAGAAACTTTGGATCCAGCACTAGTCAGATCAGGCTTCAT
TGGCAGGAAGATGGAGTTCCCCCTTGCCCAATGAAAAGACTAAGAAGTGCTTCTTTCAGATCCAAACAAGCAGGCTGACA
CTGGCCAATGACATAACCCTGGACAAGTTGATCATGGCTAATGATGACCTCTCTTGTTGCCAACGTCAAGGCAATTTATA
TAGAAGCTCGTCTGATGGCCTTGAGAGAGCATAGAATGAAGCTAACAAATGAAGACTTAAAAAAATCTAAAGAAAACGTT
CTTTATAAACCACAAGAAGGCATCCCTGAGGGGCTCTATCTC

Alignment

ORF - retro_fcat_2015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.15 %
• Parental protein coverage: 63.86 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IGVLMDDTDPLVTVMKVEKAPQETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPG
          I.VLMDDTDPLVT.MKV.K.PQETYAD.GGLDNQIQEIKESVELPL.H.EYYEEM..KP..GVIL...PG
Retrocopy IEVLMDDTDPLVTGMKVGKSPQETYADFGGLDNQIQEIKESVELPLNHLEYYEEMDMKP-QGVILDDLPG

Parental  TGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNS
          T.KTLLAKAVANQTSATFLRVV..ELIQKYLGDG.KL..ELF.VAEEHAPSIVFIDEIDAIGTKR.DSNS
Retrocopy TSKTLLAKAVANQTSATFLRVVDTELIQKYLGDGSKLIQELF*VAEEHAPSIVFIDEIDAIGTKR*DSNS

Parental  GGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEF-PLPDEKTKRRIFQIH
          ..EREIQ.TMLE.L.QLDGFD.RGD.KVIMA.N.IETLDPAL.R.G.I.RK.EF.PLP.EKTK...FQI.
Retrocopy SREREIQ*TMLEPLKQLDGFDIRGDMKVIMAAN*IETLDPALVRSGFIGRKMEF>PLPNEKTKKCFFQIQ

Parental  TSRMTLADDVTLDDLIMAKDDLS-GADIKAICTEAGLMALRERRMKVTNEDFKKSKENVLYKKQEGTPEG
          TSR.TLA.D.TLD.LIMA.DDLS..A..KAI..EA.LMALRE.RMK.TNED.KKSKENVLYK.QEG.PEG
Retrocopy TSRLTLANDITLDKLIMANDDLS>VANVKAIYIEARLMALREHRMKLTNEDLKKSKENVLYKPQEGIPEG

Parental  LYL
          LYL
Retrocopy LYL

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	34.55 RPM
SRP017611_kidney	0.00 RPM	43.08 RPM
SRP017611_liver	0.00 RPM	27.90 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_2015 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_2015 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 19 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001839	4 retrocopies	retro_amel_1536, retro_amel_1886, retro_amel_405, retro_amel_962,
Canis familiaris	ENSCAFG00000017510	2 retrocopies	retro_cfam_1238, retro_cfam_1562,
Choloepus hoffmanni	ENSCHOG00000013595	1 retrocopy	retro_chof_1954,
Cavia porcellus	ENSCPOG00000002424	1 retrocopy	retro_cpor_144,
Dasypus novemcinctus	ENSDNOG00000006458	1 retrocopy	retro_dnov_2162,
Equus caballus	ENSECAG00000003601	1 retrocopy	retro_ecab_355,
Echinops telfairi	ENSETEG00000002661	1 retrocopy	retro_etel_580,
Felis catus	ENSFCAG00000011310	8 retrocopies	retro_fcat_1444, retro_fcat_1559, retro_fcat_2015 , retro_fcat_344, retro_fcat_614, retro_fcat_691, retro_fcat_713, retro_fcat_924,
Macropus eugenii	ENSMEUG00000001526	1 retrocopy	retro_meug_623,
Myotis lucifugus	ENSMLUG00000007471	2 retrocopies	retro_mluc_2490, retro_mluc_508,
Macaca mulatta	ENSMMUG00000022990	1 retrocopy	retro_mmul_255,
Mustela putorius furo	ENSMPUG00000008150	4 retrocopies	retro_mputfur_1602, retro_mputfur_409, retro_mputfur_654, retro_mputfur_815,
Mus musculus	ENSMUSG00000021178	3 retrocopies	retro_mmus_1517, retro_mmus_1826, retro_mmus_812,
Oryctolagus cuniculus	ENSOCUG00000006231	4 retrocopies	retro_ocun_1135, retro_ocun_1212, retro_ocun_1654, retro_ocun_411,
Otolemur garnettii	ENSOGAG00000032343	2 retrocopies	retro_ogar_3014, retro_ogar_367,
Pongo abelii	ENSPPYG00000025948	9 retrocopies	retro_pabe_1059, retro_pabe_153, retro_pabe_2379, retro_pabe_2408, retro_pabe_2737, retro_pabe_2832, retro_pabe_3099, retro_pabe_825, retro_pabe_907,
Pteropus vampyrus	ENSPVAG00000010020	3 retrocopies	retro_pvam_1190, retro_pvam_350, retro_pvam_500,
Ictidomys tridecemlineatus	ENSSTOG00000001655	1 retrocopy	retro_itri_780,
Tursiops truncatus	ENSTTRG00000013582	1 retrocopy	retro_ttru_239,