RetrogeneDB ID: retro_dord_561

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_3236:30813..31335(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hsd17b12
• Ensembl ID: ENSDORG00000004834
• Aliases: None
• Description: hydroxysteroid (17-beta) dehydrogenase 12 [Source:MGI Symbol;Acc:MGI:1926967]

Sequence

>retro_dord_561
GTGCCCGCCGCCGGCTTCCTGTACTGGGTGGGCGCGAGCACGGTGGCCTACGTGGTCCTGCGCGTCTTGTGCTCGCTCTT
CACCGCCTTCCGGGTCTGGGGTGTGGGTCATGAGGCCGGGGTCGGCCCGTGGCTCGGTGCCTGGGCAGTTGTCACAGGCA
GTACTGATGGAATTGGAAAATCATATGCCGAAGAGTTAGCAAAGCGTGGAATGAAGATTGTCTTAATCAGCAGATCACAG
GATAAACTGAACCAAGTTTCCAGTGATATAAAAGAAAAATTCAAAGTGGAGACAAGGACCATTGCTGTTGATTTCAGTTC
AGAAGATATTTATGATAAAATTAAAACAGGCCTGACAGGTCTGGAAGTTGGTGTTCTAGTGAATAACGTGGGAATGTCAT
ATGAGTATCCTGAGTACTTTTTGGATGTTCCTGACTTGGACAATACTATCAAGAAACTGATAAATACACATATTCTTTCT
GTTTGTAAGGTGACCCGATTGGTGCTGCCTGGCATGGTAGAA

Alignment

ORF - retro_dord_561 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.93 %
• Parental protein coverage: 55.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VPAAGFLYWVGASTVAYVVLRVSYSLFTAFRVWGVGHEAGVGPWLGAWAXXXXXXXXXXXXXXXXLAKRG
          VPAAGFLYWVGASTVAYVVLRV..SLFTAFRVWGVGHEAGVGPWLGAWA................LAKRG
Retrocopy VPAAGFLYWVGASTVAYVVLRVLCSLFTAFRVWGVGHEAGVGPWLGAWAVVTGSTDGIGKSYAEELAKRG

Parental  RKIVLISRSQDKVNQVSSDIKEKFKVETRTIAVDFSSEDIYDKIKTGLTGLEVGVLVNNVGMSYEYPEYF
          .KIVLISRSQDK.NQVSSDIKEKFKVETRTIAVDFSSEDIYDKIKTGLTGLEVGVLVNNVGMSYEYPEYF
Retrocopy MKIVLISRSQDKLNQVSSDIKEKFKVETRTIAVDFSSEDIYDKIKTGLTGLEVGVLVNNVGMSYEYPEYF

Parental  LDVPDLDNTIKKLINTNILSVCKVTRLVLPGMVE
          LDVPDLDNTIKKLINT.ILSVCKVTRLVLPGMVE
Retrocopy LDVPDLDNTIKKLINTHILSVCKVTRLVLPGMVE

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_561 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011325	1 retrocopy	retro_cjac_2489,
Dipodomys ordii	ENSDORG00000004834	1 retrocopy	retro_dord_561 ,
Homo sapiens	ENSG00000149084	1 retrocopy	retro_hsap_3684,
Gorilla gorilla	ENSGGOG00000002003	1 retrocopy	retro_ggor_2491,
Nomascus leucogenys	ENSNLEG00000017959	1 retrocopy	retro_nleu_2273,
Oryctolagus cuniculus	ENSOCUG00000016351	1 retrocopy	retro_ocun_1335,
Otolemur garnettii	ENSOGAG00000009102	1 retrocopy	retro_ogar_3391,
Pongo abelii	ENSPPYG00000003343	1 retrocopy	retro_pabe_3021,
Pan troglodytes	ENSPTRG00000003522	1 retrocopy	retro_ptro_2499,
Ictidomys tridecemlineatus	ENSSTOG00000005473	1 retrocopy	retro_itri_1099,
Tursiops truncatus	ENSTTRG00000005103	1 retrocopy	retro_ttru_772,