RetrogeneDB ID: retro_dord_91

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_2845:266038..266478(+)
• Located in intron of: ENSDORG00000006285

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ebag9
• Ensembl ID: ENSDORG00000010177
• Aliases: None
• Description: estrogen receptor-binding fragment-associated gene 9 [Source:MGI Symbol;Acc:MGI:1859920]

Sequence

>retro_dord_91
ATGGCCATCATTCAGTTTCAGCTATTTAAAGTTTGTACTGCTTAGCAACAGTATTCTCATCCCTAAAGAGATTAAATATG
CAGGTCTGGCAGAGGAAGAAAATTAAGTGGACACCAAATAACTTTGCCAACTACAGTTGATTATTCTTCTGTTCCAAACA
GACAGATGTGGAGAAGTGCACTTTCTGGGATGAAGATGCACTCACAAGTGTAAAGACTGAAGGAGGGAATGGCAATGTGT
CATCACAACAAAATGCTTTGGACCGACTGGAACCTAACTATTTTAAGGACATGACACCAACTATAAGGAAATCTCAGAAA
ATTGTTATTAAGAAGAGAGAGCCGTTAAATTTTGGCATCCTGGATGGTAGGACAGATTTCTCCAGTAGATTAGCAGCTAT
ACAAGATATGCCTTTTATTCATCAATCACCTGAATTAGGC

Alignment

ORF - retro_dord_91 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.33 %
• Parental protein coverage: 56.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAITQFRLFKVCT-CLATVFSFLKRL-ICRSGRGRKLSGDQITLPTTVDYSSVP-KQTDVEEWTSWDEDA
          MAI.QF.LFKVCT.CLATVFS.LKRL.ICRSGRGRKLSG.QITLPTTVDYSSVP.KQTDVE..T.WDEDA
Retrocopy MAIIQFQLFKVCT<CLATVFSSLKRL>ICRSGRGRKLSGHQITLPTTVDYSSVP<KQTDVEKCTFWDEDA

Parental  PTSVKIEGGNGNVASQQNALEQLEPDYFKDMTPTIRKTQKIVIKKREPLNFGIPDGSTGFSSRLAATQDM
          .TSVK.EGGNGNV.SQQNAL..LEP.YFKDMTPTIRK.QKIVIKKREPLNFGI.DG.T.FSSRLAA.QDM
Retrocopy LTSVKTEGGNGNVSSQQNALDRLEPNYFKDMTPTIRKSQKIVIKKREPLNFGILDGRTDFSSRLAAIQDM

Parental  PFIHQSSELG
          PFIHQS.ELG
Retrocopy PFIHQSPELG

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_91 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 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006190	1 retrocopy	retro_amel_1656,
Choloepus hoffmanni	ENSCHOG00000007848	5 retrocopies	retro_chof_1116, retro_chof_1455, retro_chof_1805, retro_chof_2245, retro_chof_751,
Cavia porcellus	ENSCPOG00000001059	1 retrocopy	retro_cpor_1185,
Dipodomys ordii	ENSDORG00000010177	2 retrocopies	retro_dord_418, retro_dord_91 ,
Equus caballus	ENSECAG00000009719	2 retrocopies	retro_ecab_211, retro_ecab_232,
Felis catus	ENSFCAG00000025490	1 retrocopy	retro_fcat_777,
Macropus eugenii	ENSMEUG00000014115	3 retrocopies	retro_meug_1871, retro_meug_2058, retro_meug_597,
Monodelphis domestica	ENSMODG00000004795	2 retrocopies	retro_mdom_261, retro_mdom_665,
Mus musculus	ENSMUSG00000022339	1 retrocopy	retro_mmus_3501,
Rattus norvegicus	ENSRNOG00000004220	2 retrocopies	retro_rnor_2914, retro_rnor_2980,
Sus scrofa	ENSSSCG00000006024	1 retrocopy	retro_sscr_569,
Ictidomys tridecemlineatus	ENSSTOG00000015326	1 retrocopy	retro_itri_1119,
Tursiops truncatus	ENSTTRG00000001745	2 retrocopies	retro_ttru_496, retro_ttru_672,