RetrogeneDB ID: retro_dord_230

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_6153:25214..25810(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccnc
• Ensembl ID: ENSDORG00000008393
• Aliases: None
• Description: cyclin C [Source:MGI Symbol;Acc:MGI:1858199]

Sequence

>retro_dord_230
TTATTTCAAGAGAGATTCTATGCCAGGTATTCTCTGAAAAGTATAGATCCTGTATTATTGGCTCCTACATGTGTGTTTTT
GGCATCCAAAGTAGAGAATCTGGAGTGGTTTCTACTATGAGGTTGATTGCTGCTGCTACTTCTGTATTGAAAACTAGATT
TTCATATGCCTTCCCAAAGCAATTCCATTATAAGATGAATCATATATTAGAATGTGAATTCTATCTACTAGAACTAATGG
ATTGTTGCTTGATCGTGTATCATCCTTACAGACCTTTGCTCCAGTATGTGCAGGACATAGACCAAGAAGACACGTTGCTT
CCCCTTGCATGAAGAATAGTGAATGATACCTACAGAACGGATCTTTGCCTACTGTATCCTCCTTTCCTGATAGCTCTAGT
TTGCCTACGTGTGGCCTGTGTTGTACAGCAGAAAGATGCCAGACAGTGGTTTGCTGAACTTTCTGTGGACATGGAGAAGA
TTTGGGGAATAATCAGGGTTATTTTTAAACTGTATGAGCACTGGAAGAATTCCGATGAGAAAAAAGAAATAGCTACTATT
CTTAGTAAGATGCCAAAACCAAAACCACCTCCAAAC

Alignment

ORF - retro_dord_230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 65.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VYFKRFYARYSLKSIDPVLMAPTCVFLASKVE-EFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYKMNHI
          ....RFYARYSLKSIDPVL.APTCVFLASKVE.E.GVVS..RLIAAATSVLKTRFSYAFPK.F.YKMNHI
Retrocopy LFQERFYARYSLKSIDPVLLAPTCVFLASKVE<ESGVVSTMRLIAAATSVLKTRFSYAFPKQFHYKMNHI

Parental  LECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVND-YRTDLCLLYPPFMIALACLHVA
          LECEFYLLELMDCCLIVYHPYRPLLQYVQD..QED.LLPLA.RIVND.YRTDLCLLYPPF.IAL.CL.VA
Retrocopy LECEFYLLELMDCCLIVYHPYRPLLQYVQDIDQEDTLLPLA*RIVNDTYRTDLCLLYPPFLIALVCLRVA

Parental  CVVQQKDARQWFAELSVDMEKILEIIRVILKLYEQWKNFDEKKEMATILSKMPKPKPPPN
          CVVQQKDARQWFAELSVDMEKI..IIRVI.KLYE.WKN.DEKKE.ATILSKMPKPKPPPN
Retrocopy CVVQQKDARQWFAELSVDMEKIWGIIRVIFKLYEHWKNSDEKKEIATILSKMPKPKPPPN

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_230 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008954	1 retrocopy	retro_amel_1828,
Canis familiaris	ENSCAFG00000003525	1 retrocopy	retro_cfam_1774,
Dasypus novemcinctus	ENSDNOG00000011999	3 retrocopies	retro_dnov_1153, retro_dnov_216, retro_dnov_2243,
Dipodomys ordii	ENSDORG00000008393	2 retrocopies	retro_dord_230 , retro_dord_75,
Dipodomys ordii	ENSDORG00000012846	1 retrocopy	retro_dord_420,
Myotis lucifugus	ENSMLUG00000012815	1 retrocopy	retro_mluc_1582,
Oryctolagus cuniculus	ENSOCUG00000003309	2 retrocopies	retro_ocun_1753, retro_ocun_888,
Ochotona princeps	ENSOPRG00000012972	2 retrocopies	retro_opri_1026, retro_opri_151,
Sus scrofa	ENSSSCG00000004353	1 retrocopy	retro_sscr_760,
Tupaia belangeri	ENSTBEG00000017525	1 retrocopy	retro_tbel_677,