RetrogeneDB ID: retro_dord_70

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_1964:210320..210497(-)
• Located in intron of: ENSDORG00000002628

Retrocopy information

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

Parental gene information

• Parental gene symbol: Crip1
• Ensembl ID: ENSDORG00000001365
• Aliases: None
• Description: cysteine-rich protein 1 (intestinal) [Source:MGI Symbol;Acc:MGI:88501]

Sequence

>retro_dord_70
CTAACCTCACTGGGCAAAGACTGTCAACTGTCCTGCTTTCAGTGTGACAAATGTGGAAAGACACTGACCTCCCAGAGCCA
CGCGGTGCAAGAAGGCAAGCCCTACTGCAACCATCCAAGCTACTCTGCCATGTTTGGGTCCAAAGGCTTTGGATGGGGTG
GAGCTGAGAGTCACACT

Alignment

ORF - retro_dord_70 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.58 %
• Parental protein coverage: 76.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRGGAESHT
          .TSLGKD....C..C.KCGKTLTS..HA..EGKPYCNHP.YSAMFG.KGFG.GGAESHT
Retrocopy LTSLGKDCQLSCFQCDKCGKTLTSQSHAVQEGKPYCNHPSYSAMFGSKGFGWGGAESHT

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_70 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047229	1 retrocopy	retro_btau_488,
Callithrix jacchus	ENSCJAG00000019788	1 retrocopy	retro_cjac_163,
Dipodomys ordii	ENSDORG00000001365	1 retrocopy	retro_dord_70 ,
Homo sapiens	ENSG00000213145	1 retrocopy	retro_hsap_2550,
Gorilla gorilla	ENSGGOG00000027381	1 retrocopy	retro_ggor_3,
Macropus eugenii	ENSMEUG00000001631	1 retrocopy	retro_meug_93,
Macaca mulatta	ENSMMUG00000007158	2 retrocopies	retro_mmul_1479, retro_mmul_553,
Pongo abelii	ENSPPYG00000006209	1 retrocopy	retro_pabe_114,
Pan troglodytes	ENSPTRG00000033768	1 retrocopy	retro_ptro_43,
Pteropus vampyrus	ENSPVAG00000014240	1 retrocopy	retro_pvam_1304,
Rattus norvegicus	ENSRNOG00000027990	2 retrocopies	retro_rnor_2590, retro_rnor_2599,
Sarcophilus harrisii	ENSSHAG00000000807	1 retrocopy	retro_shar_341,
Tursiops truncatus	ENSTTRG00000004063	1 retrocopy	retro_ttru_1367,