RetrogeneDB ID: retro_dord_652

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_48471:4304..4579(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000003073
• Aliases: None
• Description: None

Sequence

>retro_dord_652
TCTGCTGTCATCACTAGAATTCTCAAGGAGGTGCTCCCAGATGGAGCCAACATCCAAGAGGCCTGAGTGCCATCTCCCGT
GCTGCCAGAGTCTTCGTGCTGTATGCCATGTCCTGTGCCAATAATTTTACATGAAAGGGAAGCGCAGACACTCAATGCCA
GTGATGTACTCCTCCGCCATTGGAGAATTGGAGTACCAACTGTTCATTACCCCCTTAAAAGAAGCTCTAGAGCTATAGGC
AGGAGTTGAAAGGCAAGAAGGAAGCTTCAGAGCAA

Alignment

ORF - retro_dord_652 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.0 %
• Parental protein coverage: 89.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  NAVITRIIKEALPDGVNISKEA-RSAISRAASVFVLYATSCANNFA-MKGKRK-TLNASDVL-SAMEEME
          .AVITRI.KE.LPDG.NI..EA..SAISRAA.VFVLYA.SCANNF..MKGKR..TLNASDVL.SA..E.E
Retrocopy SAVITRILKEVLPDGANI-QEA<LSAISRAARVFVLYAMSCANNFT<MKGKRR<TLNASDVL>SAIGELE

Parental  FQRFITPLKEALE-AYRREQKGKK-EASEQ
          .Q.FITPLKEALE.A..R..K....EASEQ
Retrocopy YQLFITPLKEALE<AIGRS*KARR<EASEQ

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_652 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017917	1 retrocopy	retro_cjac_4121,
Cavia porcellus	ENSCPOG00000000313	1 retrocopy	retro_cpor_355,
Dipodomys ordii	ENSDORG00000003073	2 retrocopies	retro_dord_526, retro_dord_652 ,
Monodelphis domestica	ENSMODG00000004358	3 retrocopies	retro_mdom_1680, retro_mdom_1920, retro_mdom_647,
Mus musculus	ENSMUSG00000028394	2 retrocopies	retro_mmus_124, retro_mmus_555,
Pteropus vampyrus	ENSPVAG00000004717	1 retrocopy	retro_pvam_302,
Rattus norvegicus	ENSRNOG00000015392	1 retrocopy	retro_rnor_55,
Ictidomys tridecemlineatus	ENSSTOG00000027365	1 retrocopy	retro_itri_866,
Tupaia belangeri	ENSTBEG00000005211	1 retrocopy	retro_tbel_4052,