RetrogeneDB ID: retro_dord_282

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_777:206378..207344(+)
• Located in intron of: ENSDORG00000016166

Retrocopy information

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

Parental gene information

• Parental gene symbol: Oxct1
• Ensembl ID: ENSDORG00000016318
• Aliases: None
• Description: 3-oxoacid CoA transferase 1 [Source:MGI Symbol;Acc:MGI:1914291]

Sequence

>retro_dord_282
GGCGTGGACGACTTCGGCCTGGGGCTCCTGCTGGCCGCCAAGCAGGTCAAGCGCGTGATCTGTTCCTACCTGGGGGAAAA
CGCGCTCTGCGAGAAGATGTACCTGGCGGGCGAGTTGGAACTGGAGATGACCCCGCAGGGCACCCTGGCCGAGCGGATCC
GCGCCGCTGGGGCCGGCGTGCCCGCCTTCTACACGCCCACCGGCTACGGGACGTTGGTGCAGGAAGGAGGTGCGCCCATG
CTCTATGGCTCGGGCGGCCACAGGCTCGCCCTGAGCCAGCCCAGAGAGGTGCGGACCTTCAACGGCCGGCACTACCTCCT
GGAGCAAGCCATCAGGGCCGACTTTGCCCTAATAAAGGCCTGGAAGGCTGACCGCTCTGGCAATGTCGTCTTTAGGGGGA
GTGCCCGGAACTTCAATGTGCCGATGTGCAAGGCCGCGGATGTCACCGTGGTGGAGGTGGAAGAGATCGTGGATGTGGGC
ACTTTTCCCAAAGAAGACGTCCATGTTCCCAACATTTATGTAGATCGCGTGATAAAGGGGCCGAAGTTTGAGAAGAGAAT
CGAGCGTTTAATCACACGAAGTGAGAAAGATGATGCCAAAGCCAAAAAGGGAGATGACATCAGAACTCGGATCATCAAAC
GTGCAGCCCTGGAATTCAAGGATGGCATGTATGCCAACCTGGGCATCGGGATCCCCGTGCTGGCCAGCAACTTCATCAGC
CCTGACATAACCGTTTTTCTGCACAGTGAGAATGGACTCCTGGGCTTGGGCCCGTTCCCATTAAAACACGAGGTGGACCC
CGATATCATCAATGCAGGCAAGCAGACAGTCACTGTGCTCCCCGGGGGCAGTTTCTTTGGCAGCGATGAGTCCTTTGCCA
TGATTCGAGGGGGCCACCTGCAACTGACCATGCTGGGTGCCATGCAGGTTTCTAAATATGGGGACCTGGCTAACTGGATG
ATACCT

Alignment

ORF - retro_dord_282 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.69 %
• Parental protein coverage: 63.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVDNFGLGLLLHSKQIKRMISSYVGENAEFERQYLSGELEVELIPQGTLAERIRAGGAGVPAFYTSTGYG
          GVD.FGLGLLL..KQ.KR.I.SY.GENA..E..YL.GELE.E..PQGTLAERIRA.GAGVPAFYT.TGYG
Retrocopy GVDDFGLGLLLAAKQVKRVICSYLGENALCEKMYLAGELELEMTPQGTLAERIRAAGAGVPAFYTPTGYG

Parental  TLVQEGGAPIKYNTDGTIAIASQPREVREFKGQQFILEEAITGDFALVKAWKADRAGNIIFRKTARNFNL
          TLVQEGGAP..Y...G.....SQPREVR.F.G....LE.AI..DFAL.KAWKADR.GN..FR..ARNFN.
Retrocopy TLVQEGGAPMLYGSGGHRLALSQPREVRTFNGRHYLLEQAIRADFALIKAWKADRSGNVVFRGSARNFNV

Parental  PMCKAARTTVVEVEEIVDVGSFAAEDIHVPKIYVHRLIKGEKYEKRIERLSVRKEKDGQSKSSKPGADVR
          PMCKAA..TVVEVEEIVDVG.F..ED.HVP.IYV.R.IKG.K.EKRIERL..R.EKD......K.G.D.R
Retrocopy PMCKAADVTVVEVEEIVDVGTFPKEDVHVPNIYVDRVIKGPKFEKRIERLITRSEKD--DAKAKKGDDIR

Parental  ERIIKRAALEFEDGMYANLGIGIPLLASNFISPDMTVHLQSENGVLGLGPYPMKHEVDADLINAGKETVT
          .RIIKRAALEF.DGMYANLGIGIP.LASNFISPD.TV.L.SENG.LGLGP.P.KHEVD.D.INAGK.TVT
Retrocopy TRIIKRAALEFKDGMYANLGIGIPVLASNFISPDITVFLHSENGLLGLGPFPLKHEVDPDIINAGKQTVT

Parental  VLPGASFFSSDESFAMIRGGHVDLTMLGAMQVSKYGDLANWMIP
          VLPG.SFF.SDESFAMIRGGH..LTMLGAMQVSKYGDLANWMIP
Retrocopy VLPGGSFFGSDESFAMIRGGHLQLTMLGAMQVSKYGDLANWMIP

Legend:

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

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_282 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033186	2 retrocopies	retro_btau_1243, retro_btau_1302,
Dipodomys ordii	ENSDORG00000016318	1 retrocopy	retro_dord_282 ,
Equus caballus	ENSECAG00000018312	1 retrocopy	retro_ecab_511,
Homo sapiens	ENSG00000083720	1 retrocopy	retro_hsap_14,
Gorilla gorilla	ENSGGOG00000025087	1 retrocopy	retro_ggor_378,
Myotis lucifugus	ENSMLUG00000009431	1 retrocopy	retro_mluc_194,
Nomascus leucogenys	ENSNLEG00000016656	1 retrocopy	retro_nleu_2438,
Oryctolagus cuniculus	ENSOCUG00000009231	1 retrocopy	retro_ocun_672,
Otolemur garnettii	ENSOGAG00000009909	2 retrocopies	retro_ogar_2773, retro_ogar_2781,
Pongo abelii	ENSPPYG00000015428	2 retrocopies	retro_pabe_336, retro_pabe_478,
Pan troglodytes	ENSPTRG00000016829	1 retrocopy	retro_ptro_140,
Rattus norvegicus	ENSRNOG00000043094	2 retrocopies	retro_rnor_2177, retro_rnor_2256,
Ictidomys tridecemlineatus	ENSSTOG00000008271	1 retrocopy	retro_itri_747,
Tarsius syrichta	ENSTSYG00000013641	1 retrocopy	retro_tsyr_1455,
Tursiops truncatus	ENSTTRG00000004331	1 retrocopy	retro_ttru_875,
Vicugna pacos	ENSVPAG00000002550	1 retrocopy	retro_vpac_556,