RetrogeneDB ID: retro_dord_508

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_24806:6111..6818(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Coq10b
• Ensembl ID: ENSDORG00000004090
• Aliases: None
• Description: coenzyme Q10 homolog B (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1915126]

Sequence

>retro_dord_508
ATAGCAGCTCAAACTGGTCACAGGGCCCTGTCAAAGGTAGTCTCGAGATGCCCGCCAAAGTCGGTGACAGCGGCCTGTGC
CCAGGTGCAGGGATCTGTGCTGAACGGAAGATATTTGGCTTCCTGTGGTATACTGAAGAACAGAACTCTTCCAGTACATA
CTTCGGTATTGCCCAAAGAGATATGTGCAAGAACTTTCTACAAAATCACTGTACCATTAGTAAACAAAAGAAAAGAATAC
TCCCAAGGAATTATACGGTATTCAATGCAGGAAATGTATGACATAGTATCAGGAATGGAGGATTGTAAGCATTTTGTTCC
TTGGTGCCAAAAAGCAGGGATCCTATCAAAGAGATCTGGATAGAGTGAAATGCAACTAGAAACTGGGTTTCCCCCTGTGT
TGGAACAATACACATCTATAGTGACCGTGGTGAAACCACATCTGGTAAAGGCATTCTGTACTGATGGGAAACTTTTCAAT
CGTTTAGAGAGCTTTAACCCAGGCATTCCTGGCTATCCAAGAACCTGACCCTGGATTTTTCAGTTTCTTTTGAATTCCAC
TCACGTCTACAGTCTTAGCTTGTCCCGTTGCTTTTTGATGAAGTTGTCAAACAAATGATAGTTGCCTTTGAAAGAAGAGC
ATGTAAGCTGCATGGTCCAAAAGCAAACATCCCTTAGGTATTAATGTTTCATGAAGTTCAGCATACA

Alignment

ORF - retro_dord_508 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAARAGQRALTKAVSRCPPKSATAGGGPAPGSARKGRYLASCGILMNRTLPVHTSILPKDICARTFFKIT
          .AA..G.RAL.K.VSRCPPKS.TA......GS...GRYLASCGIL.NRTLPVHTS.LPK.ICARTF.KIT
Retrocopy IAAQTGHRALSKVVSRCPPKSVTAACAQVQGSVLNGRYLASCGILKNRTLPVHTSVLPKEICARTFYKIT

Parental  APLINKRKEYSERRIIGYSMQEMYDVVSGMEDYKHFVPWCKKSDIISKRSGYCKTQLEIGFPPVLERYTS
          .PL.NKRKEYS...II.YSMQEMYD.VSGMED.KHFVPWC.K..I.SKRSG....QLE.GFPPVLE.YTS
Retrocopy VPLVNKRKEYSQG-IIRYSMQEMYDIVSGMEDCKHFVPWCQKAGILSKRSG*SEMQLETGFPPVLEQYTS

Parental  IVTLVKPHLVKASCTDGKLFNHLETIWRFSPGIPGYPRT-CTLDFSISFEFRSLLHSQLATLFFDEVVKQ
          IVT.VKPHLVKA.CTDGKLFN.LE....F.PGIPGYPRT..TLDFS.SFEF.S.L.S.L..L.FDEVVKQ
Retrocopy IVTVVKPHLVKAFCTDGKLFNRLES---FNPGIPGYPRT<LTLDFSVSFEFHSRLQS*LVPLLFDEVVKQ

Parental  MVAAFERRACKLYGPETNIPRELMFHEVHHT
          M..AFERRACKL.GP..NIP..LMFHEV.HT
Retrocopy MIVAFERRACKLHGPKANIP*VLMFHEVQHT

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_508 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 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004659	2 retrocopies	retro_btau_1595, retro_btau_1832,
Choloepus hoffmanni	ENSCHOG00000005807	1 retrocopy	retro_chof_1504,
Callithrix jacchus	ENSCJAG00000003971	1 retrocopy	retro_cjac_1836,
Dasypus novemcinctus	ENSDNOG00000003229	2 retrocopies	retro_dnov_1571, retro_dnov_2203,
Dipodomys ordii	ENSDORG00000004090	1 retrocopy	retro_dord_508 ,
Erinaceus europaeus	ENSEEUG00000001626	1 retrocopy	retro_eeur_401,
Felis catus	ENSFCAG00000022385	1 retrocopy	retro_fcat_1487,
Homo sapiens	ENSG00000115520	1 retrocopy	retro_hsap_3349,
Gorilla gorilla	ENSGGOG00000023373	2 retrocopies	retro_ggor_2270, retro_ggor_569,
Myotis lucifugus	ENSMLUG00000000865	1 retrocopy	retro_mluc_1236,
Macaca mulatta	ENSMMUG00000010488	1 retrocopy	retro_mmul_2434,
Monodelphis domestica	ENSMODG00000012281	1 retrocopy	retro_mdom_600,
Mus musculus	ENSMUSG00000025981	1 retrocopy	retro_mmus_3224,
Nomascus leucogenys	ENSNLEG00000006871	1 retrocopy	retro_nleu_1172,
Ochotona princeps	ENSOPRG00000010091	3 retrocopies	retro_opri_1020, retro_opri_173, retro_opri_664,
Pongo abelii	ENSPPYG00000013045	2 retrocopies	retro_pabe_2758, retro_pabe_576,
Pan troglodytes	ENSPTRG00000012772	1 retrocopy	retro_ptro_2137,
Rattus norvegicus	ENSRNOG00000014456	1 retrocopy	retro_rnor_1620,
Tarsius syrichta	ENSTSYG00000012642	2 retrocopies	retro_tsyr_1213, retro_tsyr_1666,