RetrogeneDB ID: retro_itri_308

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393283.1:8585167..8586090(-)
• Located in intron of: ENSSTOG00000003112

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC6
• Ensembl ID: ENSSTOG00000013840
• Aliases: None
• Description: zinc finger, DHHC-type containing 6 [Source:HGNC Symbol;Acc:19160]

Sequence

>retro_itri_308
GTTTGCCAAACATACAAGGCACCTTCTTTATATCATTTCAGAACATGTAACAGATGTCTGATGAAAATGGACCATCATCA
CCCTTGGATCAATAACTGTTGTGGTTACCAAAATCATGCTTTGTTCATACTTTTTTTTCTTTGAGCACCACTGTGTTTTA
TTCATGCTGCTTTCATTTTTGTTATCACTGTGTACATTCAACTTATAATTGGCTGTCCTTTGAGTGGAAAACAGTAAAGA
TTGAAATGAGTGCAGCCCAGAGAGTTCCTCTTCCAGTTGTTCCCTTCGAATTAGTTGCATTTGCTGCCACCTTGTTTGCC
TTGGGATTAACTTTAGAAACAACCATAGCTATTAGGATTGTGGTTTTTATCCAAGTGAAAAAAAAAAATTAGAAACAAAA
CATTTTGAATCATGGACTGAAGAAAAGGCTAAAGATCAAATTCAATATTACCAATTAGATGCAGTCTTTTGTTTTCCCCT
ATGATGTGGAAAGTAGTTGGAAGAACTTTAAAAAGGTATTTACATAGTCAAGGGTCCCAGAAAATGAATTGGAGTGGCCA
ATAAGAGAAGACTGTTGCCACTACAGTTTAATAATAGAACAGTGGAAACAAAAAGCATATGAGAGGGTCAGAAGTGTTTG
CTATAAAGTCATAGAAGATTATAGTCATGCCTACTGTCCATTGAATAAATGAAACAAAATCATCATAATCTTTTACACTG
AGAACCCTCAAATACAGCTACAAAAAAAGGGGAGTTCATTTATTTTAGCCACAGGGTTATAATGCTGCTTATGTGGAGAC
AGAATTCTGGGTGATTCCTTTGTAGATGTTCCAAGAATAAGAGGATGGTTCCCTAGAAACCATGTGGAAAAGTGTCCCTG
TCATGCTGAAGCAGATCTAGCCCCAGAGGACAACAAGAAAAAC

Alignment

ORF - retro_itri_308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.13 %
• Parental protein coverage: 75.06 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VCQAYKAPRSHHCRKCNRCVMKMDHHCPWINNCCGYQNHASFTLFLLLAPLGCIHAAFIFVMTMYTQL-Y
          VCQ.YKAP...H.R.CNRC.MKMDHH.PWINNCCGYQNHA.F....L.APL..IHAAFIFV.T.Y.QL.Y
Retrocopy VCQTYKAPSLYHFRTCNRCLMKMDHHHPWINNCCGYQNHALFIXXXL*APLCFIHAAFIFVITVYIQL<Y

Parental  NRLSFGWNTVKIDMSAARRDPLPIVPFGLAAFAATLFALGLALGTTIAVGMLFFIQMKIILRNKTSIESW
          N.LSF.W.TVKI.MSAA.R.PLP.VPF.L.AFAATLFALGL.L.TTIA.....FIQ..............
Retrocopy NWLSFEWKTVKIEMSAAQRVPLPVVPFELVAFAATLFALGLTLETTIAIRIVVFIQVXXXX*KQNILNHG

Parental  IEEKAK-DRIQYYQLDEV-FVFPYDMGSKWKNFTQVFTWSGVPEGDGLEWPVREDCHPYSLTIEQLKQKA
          .....K.D.IQYYQLD.V.FVFPYD..S.WKNF..VFT.S.VPE...LEWP.REDC..YSL.IEQ.KQKA
Retrocopy LKKRLK<DQIQYYQLDAV>FVFPYDVESSWKNFKKVFT*SRVPENE-LEWPIREDCCHYSLIIEQWKQKA

Parental  DKRVRSVRYKVTEDYSGSCCPLNKGIKTIFTIPCTEEPRIQLRK--GEFILATRGLRYWLYGDKILDDSF
          ..RVRSV.YKV.EDYS...CPLNK..K.I..I..TE.P.IQL.K....FILAT.GL...L.GD.IL.DSF
Retrocopy YERVRSVCYKVIEDYSHAYCPLNK*NK-IIIIFYTENPQIQLQKKGSSFILAT-GL*CCLCGDRILGDSF

Parental  AEGVSRIRGWFPRKCVEKCPCEAETDPAPEGEKKN
          ...V.RIRGWFPR..VEKCPC.AE.D.APE..KKN
Retrocopy VD-VPRIRGWFPRNHVEKCPCHAEADLAPEDNKKN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_308 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_308 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015401	1 retrocopy	retro_amel_1120,
Canis familiaris	ENSCAFG00000010960	1 retrocopy	retro_cfam_2178,
Choloepus hoffmanni	ENSCHOG00000012828	1 retrocopy	retro_chof_1480,
Felis catus	ENSFCAG00000030784	1 retrocopy	retro_fcat_1193,
Loxodonta africana	ENSLAFG00000008129	1 retrocopy	retro_lafr_304,
Mustela putorius furo	ENSMPUG00000002043	1 retrocopy	retro_mputfur_668,
Mus musculus	ENSMUSG00000024982	1 retrocopy	retro_mmus_1740,
Otolemur garnettii	ENSOGAG00000030535	1 retrocopy	retro_ogar_1652,
Ictidomys tridecemlineatus	ENSSTOG00000013840	1 retrocopy	retro_itri_308 ,
Tarsius syrichta	ENSTSYG00000009673	2 retrocopies	retro_tsyr_1653, retro_tsyr_1771,