RetrogeneDB ID: retro_dord_303

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_10780:33943..34261(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccdc12
• Ensembl ID: ENSDORG00000016567
• Aliases: None
• Description: coiled-coil domain containing 12 [Source:MGI Symbol;Acc:MGI:1919904]

Sequence

>retro_dord_303
GAACTGAGGCTGCACAGTTACTTCCCTGAGGATGAGGATCTGAAAAGGAGAAAAGTGCCCCAGGCCAAACCCATGGCAGT
GGAGGAAAAAGTGAAGGAGCAGCTGGAGACTATCATTGAAGAAATGGATCTGGCTAATCTTGCACCGAGGAAGCCTGATT
GGGACCTTAAGAGAGATGTGGCCAAGAAACTAGAAAAACTTGAAAAGAGGACCCAGAGAGCCATTGCTGAGCTGATCCGT
GAGCAGCTCAAAGGCCAGGAGGACAGCCTGGCCTCAGCCGTGAATACCCCCACAGGACAGGATGCCTGCGACTCCGAC

Alignment

ORF - retro_dord_303 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.68 %
• Parental protein coverage: 66.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELRLRNYVPEDEDLKRRRVPQAKPVAVEEKVKEQLEAAKPEPVIEEVDLANLAPRKPDWDLKRDVAKKLE
          ELRL..Y.PEDEDLKRR.V....P.A....V.E.......E..IEE.DLANLAPRKPDWDLKRDVAKKLE
Retrocopy ELRLHSYFPEDEDLKRRKV----PQAKPMAVEEKVKE-QLETIIEEMDLANLAPRKPDWDLKRDVAKKLE

Parental  KLEKRTQRAIAELIRERLKGQEDSLASAVNAPTGQEACDSD
          KLEKRTQRAIAELIRE.LKGQEDSLASAVN.PTGQ.ACDSD
Retrocopy KLEKRTQRAIAELIREQLKGQEDSLASAVNTPTGQDACDSD

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_303 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002280	3 retrocopies	retro_cjac_1212, retro_cjac_2317, retro_cjac_3225,
Dipodomys ordii	ENSDORG00000016567	1 retrocopy	retro_dord_303 ,
Echinops telfairi	ENSETEG00000000030	2 retrocopies	retro_etel_1445, retro_etel_2038,
Homo sapiens	ENSG00000160799	1 retrocopy	retro_hsap_2257,
Macaca mulatta	ENSMMUG00000019810	1 retrocopy	retro_mmul_1025,
Mus musculus	ENSMUSG00000019659	1 retrocopy	retro_mmus_1275,
Nomascus leucogenys	ENSNLEG00000006219	1 retrocopy	retro_nleu_1282,
Ochotona princeps	ENSOPRG00000005086	1 retrocopy	retro_opri_746,
Pongo abelii	ENSPPYG00000013924	2 retrocopies	retro_pabe_1957, retro_pabe_2033,
Pan troglodytes	ENSPTRG00000014862	1 retrocopy	retro_ptro_1597,
Sarcophilus harrisii	ENSSHAG00000003265	1 retrocopy	retro_shar_251,