RetrogeneDB ID: retro_dord_250

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_6715:30401..30710(+)
• Located in intron of: ENSDORG00000007641

Retrocopy information

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

Parental gene information

• Parental gene symbol: Erh
• Ensembl ID: ENSDORG00000006912
• Aliases: None
• Description: enhancer of rudimentary homolog (Drosophila) [Source:MGI Symbol;Acc:MGI:108089]

Sequence

>retro_dord_250
TCTCACACCATTTTGCTGGTGTAGCCTACCAAGAGGCCAGAAGGCAGAACTTACGCTGACTATGAATCTGTGAATGAATG
CATGGAAGGTGTTTGTAAAATGTATGAAGAACACCTGAAGAGAATGAATCCCAATAGCCCCTCGATCACGTATGATATCA
GTCAGTTGTTTGATTTTATCGACGATCTGGCAGATCTCAGTTGCCTTGTTTACCGAGCTGATACCCAGACATACCAGCCT
TATAACAAAAACTGGATCAAAGAGAAGCTCTACGTACTCCTTCGTCGGCAGGCCCAACAGGCTGGGAAA

Alignment

ORF - retro_dord_250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SHTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNPNSPSITYDISQLFDFIDDLADLSCLV
          SHTILLV.PTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNPNSPSITYDISQLFDFIDDLADLSCLV
Retrocopy SHTILLV*PTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNPNSPSITYDISQLFDFIDDLADLSCLV

Parental  YRADTQTYQPYNKDWIKEKIYVLLRRQAQQAGK
          YRADTQTYQPYNK.WIKEK.YVLLRRQAQQAGK
Retrocopy YRADTQTYQPYNKNWIKEKLYVLLRRQAQQAGK

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_250 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 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014529	1 retrocopy	retro_amel_1906,
Callithrix jacchus	ENSCJAG00000014940	2 retrocopies	retro_cjac_209, retro_cjac_846,
Dipodomys ordii	ENSDORG00000006912	3 retrocopies	retro_dord_250 , retro_dord_406, retro_dord_562,
Equus caballus	ENSECAG00000019178	1 retrocopy	retro_ecab_45,
Macropus eugenii	ENSMEUG00000014602	3 retrocopies	retro_meug_1469, retro_meug_498, retro_meug_64,
Myotis lucifugus	ENSMLUG00000011879	1 retrocopy	retro_mluc_142,
Macaca mulatta	ENSMMUG00000021571	1 retrocopy	retro_mmul_1649,
Oryctolagus cuniculus	ENSOCUG00000004636	1 retrocopy	retro_ocun_42,
Otolemur garnettii	ENSOGAG00000029388	5 retrocopies	retro_ogar_1170, retro_ogar_1537, retro_ogar_2710, retro_ogar_625, retro_ogar_854,
Rattus norvegicus	ENSRNOG00000004883	3 retrocopies	retro_rnor_1721, retro_rnor_2670, retro_rnor_308,