RetrogeneDB ID: retro_dord_81

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_2346:21646..21983(-)
• Located in intron of: ENSDORG00000009586

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000014888
• Aliases: None
• Description: None

Sequence

>retro_dord_81
CAGGTGGTGGGCAGAACCTTCGCTTGGGCCCTGCTGACAAGAATTTGCAGCTAGCCGGGCAGCAGCTGACGCCCGGGGAC
ATGCCGGGCACCAATCCGCAGCCGCATCCAACCTCTCTGGCCTCAGCCTCCAGGAGGCTCAGCAGATTCTCAACATCTCC
AAGCTGAATCCCGAGGAGGTCCAGAAGAACTATGAACACCTATTTAAAGTGAACGATAAATCTGTAGGTGGCTCCTTCTA
CCTGCAGTCAAAGGTTGTCCGGGCCGAGGAGCGTCTGGATGAGGAGCTCAGAATCCAGGCCCAAGAAGACAGAGAGAAAG
GGACGACACCCAAAACG

Alignment

ORF - retro_dord_81 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.81 %
• Parental protein coverage: 89.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QVVGRAFARALR-QEFAASQAAADARGRAGHQSAAASNLSGLSLQEAQQILNISKLNPEEVQKNYEHLFK
          QVVGR.FA.AL..QEFAAS.AAADARG.AGHQSAAASNLSGLSLQEAQQILNISKLNPEEVQKNYEHLFK
Retrocopy QVVGRTFAWALL>QEFAASRAAADARGHAGHQSAAASNLSGLSLQEAQQILNISKLNPEEVQKNYEHLFK

Parental  VNDKSVGGSFYLQSKVVRAKERLDEELRIQAQEDREKGTTPKT
          VNDKSVGGSFYLQSKVVRA.ERLDEELRIQAQEDREKGTTPKT
Retrocopy VNDKSVGGSFYLQSKVVRAEERLDEELRIQAQEDREKGTTPKT

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_81 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 16 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009200	1 retrocopy	retro_btau_1664,
Canis familiaris	ENSCAFG00000019226	1 retrocopy	retro_cfam_1967,
Callithrix jacchus	ENSCJAG00000019772	1 retrocopy	retro_cjac_1148,
Dasypus novemcinctus	ENSDNOG00000010921	2 retrocopies	retro_dnov_1361, retro_dnov_8,
Dipodomys ordii	ENSDORG00000014888	1 retrocopy	retro_dord_81 ,
Equus caballus	ENSECAG00000019387	1 retrocopy	retro_ecab_302,
Erinaceus europaeus	ENSEEUG00000007432	7 retrocopies	retro_eeur_138, retro_eeur_171, retro_eeur_213, retro_eeur_234, retro_eeur_273, retro_eeur_440, retro_eeur_673,
Echinops telfairi	ENSETEG00000006416	1 retrocopy	retro_etel_2070,
Felis catus	ENSFCAG00000027971	1 retrocopy	retro_fcat_520,
Myotis lucifugus	ENSMLUG00000008921	6 retrocopies	retro_mluc_2446, retro_mluc_2447, retro_mluc_2448, retro_mluc_2516, retro_mluc_2517, retro_mluc_429,
Mus musculus	ENSMUSG00000014301	1 retrocopy	retro_mmus_73,
Rattus norvegicus	ENSRNOG00000004608	1 retrocopy	retro_rnor_713,
Sus scrofa	ENSSSCG00000007947	2 retrocopies	retro_sscr_1090, retro_sscr_468,
Ictidomys tridecemlineatus	ENSSTOG00000003461	1 retrocopy	retro_itri_1732,
Tupaia belangeri	ENSTBEG00000001347	1 retrocopy	retro_tbel_3190,
Tarsius syrichta	ENSTSYG00000009306	1 retrocopy	retro_tsyr_282,