RetrogeneDB ID: retro_dord_532

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_27828:7159..7619(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000008703
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hsd17b10
• Ensembl ID: ENSDORG00000004051
• Aliases: None
• Description: hydroxysteroid (17-beta) dehydrogenase 10 [Source:MGI Symbol;Acc:MGI:1333871]

Sequence

>retro_dord_532
CTGACTGCAGCATGCCGGAGCGTGAAGGGCTTGGATGCTACCATAACCGGAGGAGCCTCTGGCCTTGGCCTGGCCACGGC
CGCGCGATGGGTGAAACAGGGGCCACGGCTGTGCTTCTGGACTTGTCCGACTCCAGTGGTGAGGCCCAGGCCAAGAAGTT
AGGAAAGGGCTGCATGCTCGCCCCAGCCGATGTAACCTCTGAGAAGGACGTTCAAGCAGCCCTGAATCTAGCCAAAGAAA
AGTTTGGCCGTGTAAATGTGGCGGTCAACGGTGCAGGTACTGCAGTGGCCATTAAGACATACAATGCAAAGAAGAACGTG
GCCCATACTTTGGAGGAGTTCCAGCAAGTTCTCAATGTGAATCTCATAGGCACCTTCAATGGGATCCGCTCGGCTGCTAG
TGAGATGGAGCCAGAATGAAGCAGACCTAAGGAGACGAACGTGGGGTTATCATCAACACT

Alignment

ORF - retro_dord_532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 77.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAACRSVKGLVAIITGGASGLGLATAERLVKQG-ATAVLLDLSDSDGEAQAKKLGKGCVFAPADVTSEK
          ..AACRSVKGL.A.ITGGASGLGLATA.R.VKQG.ATAVLLDLSDS.GEAQAKKLGKGC..APADVTSEK
Retrocopy LTAACRSVKGLDATITGGASGLGLATAARWVKQG<ATAVLLDLSDSSGEAQAKKLGKGCMLAPADVTSEK

Parental  DVQAALNLAKEKFGRVDVAVNCAGIAVAIKTYNAKKNMAHTLEDFQRVLNVNLVGTFNVIRLAASEM-GQ
          DVQAALNLAKEKFGRV.VAVN.AG.AVAIKTYNAKKN.AHTLE.FQ.VLNVNL.GTFN.IR.AASEM..Q
Retrocopy DVQAALNLAKEKFGRVNVAVNGAGTAVAIKTYNAKKNVAHTLEEFQQVLNVNLIGTFNGIRSAASEM>SQ

Parental  NEADQ-GGERGVIINT
          NEAD..G.ERGVIINT
Retrocopy NEADL>GDERGVIINT

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_532 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005036	1 retrocopy	retro_amel_371,
Canis familiaris	ENSCAFG00000016277	1 retrocopy	retro_cfam_545,
Choloepus hoffmanni	ENSCHOG00000000939	1 retrocopy	retro_chof_582,
Cavia porcellus	ENSCPOG00000009594	1 retrocopy	retro_cpor_535,
Dipodomys ordii	ENSDORG00000004051	1 retrocopy	retro_dord_532 ,
Erinaceus europaeus	ENSEEUG00000005080	1 retrocopy	retro_eeur_379,
Felis catus	ENSFCAG00000013899	1 retrocopy	retro_fcat_1827,
Macropus eugenii	ENSMEUG00000008565	1 retrocopy	retro_meug_2184,
Myotis lucifugus	ENSMLUG00000000175	1 retrocopy	retro_mluc_4,
Otolemur garnettii	ENSOGAG00000002951	1 retrocopy	retro_ogar_1823,
Tarsius syrichta	ENSTSYG00000005340	3 retrocopies	retro_tsyr_1000, retro_tsyr_1542, retro_tsyr_2078,
Xenopus tropicalis	ENSXETG00000007721	1 retrocopy	retro_xtro_39,