RetrogeneDB ID: retro_itri_1054

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393364.1:1310166..1311165(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC4
• Ensembl ID: ENSSTOG00000011605
• Aliases: None
• Description: zinc finger, DHHC-type containing 4 [Source:HGNC Symbol;Acc:18471]

Sequence

>retro_itri_1054
ATGAACTTCCTGGTTCTCTTCTTGTTCTACCTGGTGTTTGAACTGATTTGTGTTGTTATGATCTGCATCTGCTAGAAAAC
CCATTGTTTGCAAGTCTGATCCAGGAAGAAGCACAAATATGTTCCTGCATAATTCTAGGATGCCTTCAGAGAGCCATGCA
AAAATTCCTTCATTGCCCCTGTCAGACAGGTAACATTATCTTGCACCTGATCTTTCAAGGGATGGTTTATACAGAATACA
CCTGGGAAATATTCGGCTACTGTCAAGAGTTGAAGTTCTCCTGGTATCACCCTCTTCTGTCCTATCAGTTGCTGACCGTG
AGCCTGTCTTCTCCACCCTAATTGTTTAAACTATCTTGGCTCCATAACAAAAGCAAATGGATTACTATATTTTCAACTTT
ATGAATTTGATGAAGTGATGTTTCCCCAAAATATGAGGTACTCAACTGTGACTTGATGAAACCAGATCCATCAAAGCACA
GTTGTGTGTGTAACTGTTTGCAAATTGTTTTGACCATCACTGTGTTTGGATGAACAACTGAATCAGGCTGGAGTACTGGG
TACTTCTTCTTCTTCATTAATATTGAAGTCAGCTGCCACCATGGCCATTGTGAGTACCACATTTCTGATATGCTTGTTGA
TAGAGTCAGATCTATACCAGGAAACTTACCTTGATAACCTTGAATACCCCCGGGGTTTTGGACATGGACTTTCCTACTTA
GTACCTGTTCCTGTACTTTGCAGTGATTATCTTTTTGCTGGGCTTTTTCGTGGTCCTGAGCTGTCTCTTGGGGGTGTTCT
TCGCTCTGTACCTGGCAGCCACCAACCAGATCACAAATGAGTGGAACAGTTGCAACTGGAGCTGGTGCCAGTATTGCCAT
GTTGTGGCTTGGTCCCAGTTGGTGGACCCCACATCTACCAGGACATTCACTCCCCTGGCCTTTGGGGCTATCTTCAATAG
ATCTTTCTATCTTCTGTCCCATACGATAAGAAAAAGAAG

Alignment

ORF - retro_itri_1054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.26 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MDFLILFLFYLVFMLVSVVMVCICSKTNRLK-GLVQGGAQICSCIIPECIQRAVRKLLHYLFHTRNHAFI
          M.FL.LFLFYLVF.L..VVM.CIC.KT..L...L.Q..AQICSCII..C.QRA..K.LH....T.N...I
Retrocopy MNFLVLFLFYLVFELICVVMICIC*KTHCLQ<SLIQEEAQICSCIILGCLQRAMQKFLHCPCQTGN---I

Parental  ILHLVLQGTVYTEYTWEIFGYCQELEFSLYYLLLPYLLLIICL-IFFTL-TCLTNPGTITKENELLFLQV
          ILHL..QG.VYTEYTWEIFGYCQEL.FS.Y..LL.Y.LL...L..F.TL..CL...G.ITK.N.LL..Q.
Retrocopy ILHLIFQGMVYTEYTWEIFGYCQELKFSWYHPLLSYQLLTVSL<VFSTL<NCLNYLGSITKANGLLYFQL

Parental  YEFDEVMFPKNARCST-CDLRKPARSKHCSVCNWC-VHRFDHHCVWVNTCIGAWNTRYFLIYLL-TLTAS
          YEFDEVMFP.N.R.ST.CDL.KP..SKH..VCN......FDHHCVW.N..I......Y....LL..L...
Retrocopy YEFDEVMFPQNMRYST<CDLMKPDPSKHSCVCNCL<ANCFDHHCVWMNN*I---RLEYWVLLLL<SLILK

Parental  AA-VMAIISTMFLVRLVTMSDLYQETYIDDLGHSQ-AVDTAFLIQYLFLTFPRIVFLLGFVMVLSFLLGG
          .A..MAI.ST.FL..L...SDLYQETY.D.L.......D..F...YLFL.F..I.FLLGF..VLS.LLG.
Retrocopy SAATMAIVSTTFLICLLIESDLYQETYLDNLEYPR>VLDMDFPT*YLFLYFAVIIFLLGFFVVLSCLLGV

Parental  YLCFALYLAATNQTTNEWYKGDWAWCQLCPVVV-RPPSAEPQIYQNIHSHGLWSNLREIFLPAVPYYERK
          ...FALYLAATNQ.TNEW....W.WCQ.C.VV....P...P.IYQ.IHS.GLW..L..IFL..VPY...K
Retrocopy F--FALYLAATNQITNEWNSCNWSWCQYCHVVA<LVPVGGPHIYQDIHSPGLWGYLQ*IFLSSVPYDKKK

Parental  K
          K
Retrocopy K

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_1054 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1054 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009547	1 retrocopy	retro_btau_643,
Dasypus novemcinctus	ENSDNOG00000009165	1 retrocopy	retro_dnov_2610,
Homo sapiens	ENSG00000136247	1 retrocopy	retro_hsap_1193,
Macaca mulatta	ENSMMUG00000015545	1 retrocopy	retro_mmul_1283,
Nomascus leucogenys	ENSNLEG00000015607	1 retrocopy	retro_nleu_2081,
Pongo abelii	ENSPPYG00000017352	1 retrocopy	retro_pabe_993,
Pan troglodytes	ENSPTRG00000018915	1 retrocopy	retro_ptro_3038,
Pteropus vampyrus	ENSPVAG00000016104	2 retrocopies	retro_pvam_1175, retro_pvam_758,
Ictidomys tridecemlineatus	ENSSTOG00000011605	1 retrocopy	retro_itri_1054 ,
Tursiops truncatus	ENSTTRG00000005001	1 retrocopy	retro_ttru_179,
Vicugna pacos	ENSVPAG00000011480	1 retrocopy	retro_vpac_177,