RetrogeneDB ID: retro_fcat_100

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B2:24560556..24561567(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000028350
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM50A
• Ensembl ID: ENSFCAG00000011399
• Aliases: None
• Description: family with sequence similarity 50, member A [Source:HGNC Symbol;Acc:18786]

Sequence

>retro_fcat_100
ATGGCGCAGTACAAGGGCACGATGCGGGAGGCCGGCCGGGCCATGCACCTGATCAAGAAGCGGGAAAAGCAGAAGGAGCA
GATGGAGGTGCTGAAGCAGCGGATCGCCGAGGAGACCCTCATCAAGTCGAAGGTGGACAAGAAATTCTCGGCTCATTACG
ACGCCGTGGAGGCCGAGCTGAAGTCGAGCACGGTGGGCCTGGTGACCCTGAACGACATGAAGGCCAAGCAGGAGGCCCTG
CTCAAGGAGCGGGAGATGCAGCTGGCCAAGAGGGAGCAGCTGGAGGCGCGGCGGCTGCAGCTGGAGGCACTGCGGGAGAA
GGAGCGTAAGCAGGAGCAGAAGCGAAAGATCTGCAGCCTGTCCTTCACGCTCGACGAGGGCGACGAGGGCAACGTGGATG
AGGAGGTGGCGGCTAGGGAGCAGCCCACGTCGGCGGGGCTGAGCAAGAAGAAGAACCTGGGGAAGAATCCAGATGTGGAC
ACGAGCTTCCTGCCTGACCGCGACCGCGAGGAGGAGGAGAACCGGCTGCGGGAGCAGCTGCGGCAGGAGTGGGAGGCCAG
GCGCGACAAGGTGAAGCGCGAGGAGATGGAGGTCACGTTCAGCTACTGGGACGGCTCCGGGCACCGGCGCACGGTGCGCA
TCCACAAGGGTGGCACCGTGCAGCAGTTCCTGAAAAGGGCCCTGCAGGGGCTGCGAAAGGACTTCCGTGAGCTGCGGTCG
GCGGGCGTGGAGCAGCTCATGTACATCAAGGAGGACCTGATCCTGCCCCACTACCACACCTTCTACGACTTCATCGTCAC
CAAGGCCCGGGGCAAGAGTGGGCCGCTCTTCAACTTCGACGTGCACGATGACGTGCGGCTGCTGAGCGACGCCACCATGG
AAAAGGATGAGTCACACGCGGGCAAGGTGGTGCTGCGGAGCTGGTACGAGAAGAACAAGCACATCTTCCCCGCGAGCCGC
TGGGAACCCTACGACCCTGAAAAGAAGTGGGACAAGTACACGATCCGATGA

Alignment

ORF - retro_fcat_100 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.99 %
• Parental protein coverage: 99.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQYKGAASEAGRAMHLMKKREKQREQMEQMKQRLPQENIMKSNIDKKFSAHYDAVEAELKSSTVGLVTL
          MAQYKG...EAGRAMHL.KKREKQ.EQME..KQR...E...KS..DKKFSAHYDAVEAELKSSTVGLVTL
Retrocopy MAQYKGTMREAGRAMHLIKKREKQKEQMEVLKQRIAEETLIKSKVDKKFSAHYDAVEAELKSSTVGLVTL

Parental  NDMKAKQEALVKEREKQLAKKEQSKELQLKLEKLREKERKKEAKRKISSLSFTLEEEEEAGDEDEEVAVY
          NDMKAKQEAL.KERE.QLAK.EQ.....L.LE.LREKERK.E.KRKI.SLSFTL.E..E.G..DEEVA..
Retrocopy NDMKAKQEALLKEREMQLAKREQLEARRLQLEALREKERKQEQKRKICSLSFTLDEGDE-GNVDEEVAA-

Parental  EEELEREEITAKKRKLGKNPDVDTSFLPDRDREEEENRLREELRQEWEAKQEKIKSEEIEITFSYWDGSG
          ..E........KK..LGKNPDVDTSFLPDRDREEEENRLRE.LRQEWEA...K.K.EE.E.TFSYWDGSG
Retrocopy -REQPTSAGLSKKKNLGKNPDVDTSFLPDRDREEEENRLREQLRQEWEARRDKVKREEMEVTFSYWDGSG

Parental  HRRTVKMKKGNTMQQFLQKALEILRKDFSELRSAGVEQLMYIKEDLIIPHHHSFYDFIVTKARGKSGPLF
          HRRTV...KG.T.QQFL..AL..LRKDF.ELRSAGVEQLMYIKEDLI.PH.H.FYDFIVTKARGKSGPLF
Retrocopy HRRTVRIHKGGTVQQFLKRALQGLRKDFRELRSAGVEQLMYIKEDLILPHYHTFYDFIVTKARGKSGPLF

Parental  NFDVHDDVRLLSDATVEKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTV
          NFDVHDDVRLLSDAT.EKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYT.
Retrocopy NFDVHDDVRLLSDATMEKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTI

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	25.71 RPM
SRP017611_kidney	0.00 RPM	34.73 RPM
SRP017611_liver	0.00 RPM	12.54 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_100 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_100 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 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000273	1 retrocopy	retro_amel_15,
Felis catus	ENSFCAG00000011399	1 retrocopy	retro_fcat_100 ,
Homo sapiens	ENSG00000071859	1 retrocopy	retro_hsap_94,
Loxodonta africana	ENSLAFG00000008766	1 retrocopy	retro_lafr_43,
Myotis lucifugus	ENSMLUG00000022234	1 retrocopy	retro_mluc_7,
Mustela putorius furo	ENSMPUG00000009476	1 retrocopy	retro_mputfur_145,
Mus musculus	ENSMUSG00000001962	1 retrocopy	retro_mmus_103,
Nomascus leucogenys	ENSNLEG00000014266	1 retrocopy	retro_nleu_109,
Rattus norvegicus	ENSRNOG00000045790	1 retrocopy	retro_rnor_214,
Sorex araneus	ENSSARG00000006465	1 retrocopy	retro_sara_554,
Sus scrofa	ENSSSCG00000025303	1 retrocopy	retro_sscr_56,
Ictidomys tridecemlineatus	ENSSTOG00000004448	10 retrocopies	retro_itri_105, retro_itri_1563, retro_itri_1688, retro_itri_1691, retro_itri_1693, retro_itri_1758, retro_itri_1760, retro_itri_1762, retro_itri_1780, retro_itri_184,