RetrogeneDB ID: retro_fcat_1967

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:18603296..18604989(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF168
• Ensembl ID: ENSFCAG00000022131
• Aliases: None
• Description: ring finger protein 168, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:26661]

Sequence

>retro_fcat_1967
ATGGCCGCGCCCCAAAACGGCATCCCTTCCTTGTCGGAATGCCAGTGCCTCATCTGTCTGGAAATCTTAATCGAGCCCGT
AACTCTGCCTTGTAACCACACACTCTGTAATGAATGTTTCCAGTCAACTATCGAAAAGGCAAGTTTATGCTGTCCTTTCT
GTCGCCGCCGGATCTCTTCGTGGACCCGGTACCATGCCCGAAGAAATTCTCTTGTCAACCAGGAACTGTGGCAGATAATT
CAAAAACACTATCCAGAAGAATGCAGGCTTAGAATGGCTGGGCAGAAATCAGAGGAGATGGTTGATGACTTTAAGCCAGT
TCACTTATTAAGTAAGCCCGGGGAATTGAGAAAAGAATATGAAGAGGAGGTAAGAAAGATGGAGGCAGAGCGACGAGCCA
TTGAAGAAAATGAAGAAAAAATGAGTAAAGAATACATACAGAGATTATTGGCAGAAGAAGAAGAGGAGGAAAGACGGCAG
TCACAAAAAAGGCAGAAAGAGCTGGAGGAACAACTGAAAAGTGATGAAGAACTAGCAAGAAAGCTAAGCTTTAATCTTAA
TTACTGTGACAGAAAGGACTTGGCTTCTCCTTTGAATTCCACAAAACCTGGTACGGTCACAGCCAAGTATCCAAAGAAAA
GTAAGAAGAGAAACACCAACACTGGAGATATTCAGACATACTTCTCACCTAAATTTCAGTTTGGGTCAACATCACGGTCT
GAAGTTGCCCAAGAAAGCAGGAATGTCTCCATGTCCAAGGAAACTGACAATACTGTGGTAAAAAGCCCTGTGTGGCAAGA
TACAGTAAGTGAAGAAGATATGCCAACAGTTTTTCCACAACTATCCATGGACATTAAAGAACAGGCTGCACAGTCTTCAG
TAGAGTCACCTGTACCTCAGTTGCATGACAACGGTAGAGAATGGTGCCTTCAACAAAAAATTAAAATGACACGAAGCAAT
CGTGATAAAGAGTTACATGTCCTAAATAACAAGGGACCTGAAGCCAGAGTTCCCTGCTTTGGAGAAACAGAGAGTGCATG
CACTGTATCAGGTATGACACAGATAATTGAAAGTAACAAAGTTGACACAGAAAGTGAAGACGATTGCCTACTGATCAGTG
AAGATATTTCCAAAGGAAAAAACCAGGAATCTTTGTTTGAAGCAGTCACGGATCCATGCATTTCTGCAAAAAGAAAGAAA
ATGTTCCCCAAAGCTTCCACAGCTCCAGAGGAAACAGAAATCAACGTTACCGAGAATGTCATAGATTTGGAATGCTTGCC
TTCTGAGAGAAATAAACAGGAAGAGCAGGACTGGTTTTTTGCATATCAGCTTCAGCAAGAAATAGACAAAGAACAAATGA
AACCCAACCGGCAAAAAGGGTCCCCAGATGAATATCAGCTACGTCCTATATCTTCACTTCCAGACAAATTGCGAAGTGGG
CAGAGGAAGTATTCCAAAGACCAGAAGTTCAAAAAACAGACTGATAGAGAGCATTTAAAATCTCGGAGAGGCTCAGAAAA
TGAAAACTGACAGCCATCTCTTAAGATCCAGTTGAAACATTCAGTTAATGTTAACAGGAGAAAGATACCAAATCCTTCTA
CAGATAATTGTAATGTATCTAAAAGGGCTCATTCCCTACCATCTAGTAAGTCACAGACAAGTATTTTTCAGATGTTTCAG
AGGTATGGAAAGT

Alignment

ORF - retro_fcat_1967 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.97 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVTQNAIPSLSECQCRICVEILIEPITLPCNHTLCNPCFQATVEKASLCCPFCRRRVSSWTRYHTRRNS
          MA..QN.IPSLSECQC.IC.EILIEP.TLPCNHTLCN.CFQ.T.EKASLCCPFCRRR.SSWTRYH.RRNS
Retrocopy MAAPQNGIPSLSECQCLICLEILIEPVTLPCNHTLCNECFQSTIEKASLCCPFCRRRISSWTRYHARRNS

Parental  LVNMELWEIIQKHYPKECKLRVSGQESEEIVDDYQPVRLLSKPGELRREYEEEISKVEAERRASEEEENK
          LVN.ELW.IIQKHYP.EC.LR..GQ.SEE.VDD..PV.LLSKPGELR.EYEEE..K.EAERRA.EE.E.K
Retrocopy LVNQELWQIIQKHYPEECRLRMAGQKSEEMVDDFKPVHLLSKPGELRKEYEEEVRKMEAERRAIEENEEK

Parental  ASEAYIQRLLAEEEEEEKQQAEKRRREMEEQLKSDEELARKLSININNFCDGSVLTSPLNSRKSDTVTTK
          .S..YIQRLLAEEEEEE..Q..KR..E.EEQLKSDEELARKLS.N.N..CD...L.SPLNS.K..TVT.K
Retrocopy MSKEYIQRLLAEEEEEERRQSQKRQKELEEQLKSDEELARKLSFNLN-YCDRKDLASPLNSTKPGTVTAK

Parental  SQKKSKNKQTNTGDIQKYLSPKSQFGSASQCEVVQESKENSMSKETDGSIVNSPTRQDTEIEEDMPTLSP
          ..KKSK...TNTGDIQ.Y.SPK.QFGS.S..EV.QES...SMSKETD...V.SP..QDT..EEDMPT..P
Retrocopy YPKKSKKRNTNTGDIQTYFSPKFQFGSTSRSEVAQESRNVSMSKETDNTVVKSPVWQDTVSEEDMPTVFP

Parental  QIGMDVQEQGAKSSVESPMPQLYASGREWCLEAEVKMRPSNHDKELCVLNHEGPEARVPCSGETESACTI
          Q..MD..EQ.A.SSVESP.PQL...GREWCL....KM..SN.DKEL.VLN..GPEARVPC.GETESACT.
Retrocopy QLSMDIKEQAAQSSVESPVPQLHDNGREWCLQQKIKMTRSNRDKELHVLNNKGPEARVPCFGETESACTV

Parental  SGMTQIIESNTVETENEDSCLLTSKDTSKRKNQESSFEAVRDPCISAKRRKMFPRASSDQEETEINFTQK
          SGMTQIIESN.V.TE.ED.CLL.S.D.SK.KNQES.FEAV.DPCISAKR.KMFP.AS...EETEIN.T..
Retrocopy SGMTQIIESNKVDTESEDDCLLISEDISKGKNQESLFEAVTDPCISAKRKKMFPKASTAPEETEINVTEN

Parental  LIDLERLLFERHKQEEQDRLLALQLQKQVDKEQMKPNRQKGSPDEYQLRPTSSPPDKLLNGQRKNSKDRN
          .IDLE.L..ER.KQEEQD...A.QLQ...DKEQMKPNRQKGSPDEYQLRP.SS.PDKL..GQRK.SKD..
Retrocopy VIDLECLPSERNKQEEQDWFFAYQLQQEIDKEQMKPNRQKGSPDEYQLRPISSLPDKLRSGQRKYSKDQK

Parental  FKRQTDIEHSESRRGSKNENWQPSFKIQLKHSVNVNGRKVPNSSRDNCNVSKSAHSLQPSKSQKSI-FRC
          FK.QTD.EH..SRRGS.NEN.QPS.KIQLKHSVNVN.RK.PN.S.DNCNVSK.AHSL..SKSQ.SI.FRC
Retrocopy FKKQTDREHLKSRRGSENEN*QPSLKIQLKHSVNVNRRKIPNPSTDNCNVSKRAHSLPSSKSQTSI>FRC

Parental  FRGIRS
          FRG..S
Retrocopy FRGMES

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	35.69 RPM
SRP017611_kidney	0.00 RPM	15.87 RPM
SRP017611_liver	0.00 RPM	10.51 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1967 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1967 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013317	1 retrocopy	retro_btau_1816,
Felis catus	ENSFCAG00000022131	1 retrocopy	retro_fcat_1967 ,
Loxodonta africana	ENSLAFG00000010864	1 retrocopy	retro_lafr_1181,
Myotis lucifugus	ENSMLUG00000012066	1 retrocopy	retro_mluc_1315,
Ictidomys tridecemlineatus	ENSSTOG00000021829	1 retrocopy	retro_itri_683,