RetrogeneDB ID: retro_dord_200

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_5238:38128..38507(-)
• Located in intron of: ENSDORG00000003943

Retrocopy information

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

Parental gene information

• Parental gene symbol: Zcchc17
• Ensembl ID: ENSDORG00000004128
• Aliases: None
• Description: zinc finger, CCHC domain containing 17 [Source:MGI Symbol;Acc:MGI:1919955]

Sequence

>retro_dord_200
ATGAATTCAGGGAGAGCTGAGCTCATGGAAAACTTGGCTGTGCTCTACATGATTTTCCAAGGAGAGGTTGCTATGGTGAC
AGACTGTGGAGCCTTTATCAAAATCTCAGGATGTGAGAAGCAAGGTCTGGTCCATTGAACTCACATTTCATCCTGTTGAC
ATGTTGATAAGCCCTCTGAGATAGTAGCTGTTGGAGACAAAGTGTGGGTGAAGCTTATTGGTTGAGAGATGAAAAATGAT
AGGATATAAGTATCCCTTTCCATGAAAGTTGTCAACCAAGGAACTGGGAAAGACCTTGATCCTAACAATGTTATCACTGA
GCAAGAAGAGAGGTGGAAGTAGTCCTTCCAGGATTACACAGGGGCAGAAGTTCACCCTT

Alignment

ORF - retro_dord_200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.46 %
• Parental protein coverage: 52.08 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNSGRPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSC-RVDKPSEIVDVGDKVWV
          MNSGR.E.MENL..LY.IFQGEVAMVTD.GAFIKI.GC.KQGLVH.TH.SSC..VDKPSEIV.VGDKVWV
Retrocopy MNSGRAELMENLAVLYMIFQGEVAMVTDCGAFIKISGCEKQGLVH*THISSC*HVDKPSEIVAVGDKVWV

Parental  KLIGREMKNDRIKVSLSMKVVNQGTGKDLDPNNVIIEQEERRRRSFQDYT-GQKITL
          KLIG.EMKNDRI.VSLSMKVVNQGTGKDLDPNNVI.EQEER...SFQDYT.GQK.TL
Retrocopy KLIG*EMKNDRI*VSLSMKVVNQGTGKDLDPNNVITEQEERWK*SFQDYT>GQKFTL

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_200 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017710	1 retrocopy	retro_amel_1501,
Bos taurus	ENSBTAG00000016818	2 retrocopies	retro_btau_168, retro_btau_273,
Canis familiaris	ENSCAFG00000011131	2 retrocopies	retro_cfam_485, retro_cfam_835,
Callithrix jacchus	ENSCJAG00000006259	1 retrocopy	retro_cjac_4218,
Dasypus novemcinctus	ENSDNOG00000000509	1 retrocopy	retro_dnov_2548,
Dipodomys ordii	ENSDORG00000004128	1 retrocopy	retro_dord_200 ,
Myotis lucifugus	ENSMLUG00000000594	1 retrocopy	retro_mluc_2176,
Monodelphis domestica	ENSMODG00000017082	1 retrocopy	retro_mdom_252,
Mustela putorius furo	ENSMPUG00000015442	1 retrocopy	retro_mputfur_680,
Sorex araneus	ENSSARG00000007944	1 retrocopy	retro_sara_691,
Tursiops truncatus	ENSTTRG00000014870	2 retrocopies	retro_ttru_1383, retro_ttru_1613,