RetrogeneDB ID: retro_dord_792

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_9909:37773..38721(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000013152
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Sephs1
• Ensembl ID: ENSDORG00000014119
• Aliases: None
• Description: selenophosphate synthetase 1 [Source:MGI Symbol;Acc:MGI:1923580]

Sequence

>retro_dord_792
GCAGCCTTTCCCACCCTGAGCATTGGGATGGACTCGTGCGTCATCCCGCTGAGGCACGGGGGTCTGTCGCTGATACAGAC
CACTGACTTCTTTTACCCCTTGGTCGAAGATCCTTACATGATGGGGCGAATCGCGTGTGCCAACGTGCTGAGTGACCTCT
ACGCCATGGGCATTACTGAATGTGACAACATGCTAATGTTACTCAGCGTCAGCCAGAGTATGAGTGAGGAGGAACGAGAG
AAGGTGACACCGCTCATGGTCAAAGGCTTTCGGGATGCTGCTGAGGAGGGAGGAACCGCAGTGACGGGTGGACAGACAGT
GGTCAACCCCTGGATTATCATCGGTGGGGTGGCCACTGTGGTATGTCAGCCCAATGAGTTCATCATGCCTGACAGCGCTG
TGGTAGGAGATGTGCTCGTGTTGACCAAACCCTTAGGAACCCAGGTTGCCGTCAATGCCCACCAATGGTTGGATAACCCC
GAAAGGTGGGGTAAGATAAAGATGGTAGTCTCGAAAGAGGAAGTCGAGCTGGCCTATCAGGAAGCCATGTTCAATATGGC
TACCCTAAACAGAACTGCCGCTGGGTTAATGCACACATTTAATGCCCATGCAGCCACCGATATCACGGGCTTTGGCATCT
TAGGACACTCTCAGAATCTGGCAAAACAGCAGAGGAACGAGGTGTCTTTTGTCATTCATAATCTGCCAATCATCGCCAAG
ATGGCTGCCGTCAGCAAGGCCAGTGGGCGGTTCGGACTCCTCCAAGGAACCTCATCTGAAACCTCTGGGGGACTGCTCAT
TTGTCTGCCAAGAGAACAGGCAGCCCGCTTCTGTTCTGAAATCAAATCTTCAAAGTATGGAGAGGGTCACCAAGCTTGGA
TTGTCGGCATCGTGGAAAAGGGAAACAGGACGGCTCGGATCATTGACAAGCCTCGAGTTATTGAGGTT

Alignment

ORF - retro_dord_792 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.13 %
• Parental protein coverage: 81.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVMPRLXXXXXXXXIPLRHGGLSWVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGV
          A..P.L........IPLRHGGLS..QTTD..YP.V.DPYMMGRIACANVLSDLYAMG.TECDNMLMLL.V
Retrocopy AAFPTLSIGMDSCVIPLRHGGLSLIQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSV

Parental  SNKMTDRERDKVIPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLV
          S..M...ER.KV.PL...GF.DAAEE.GT.VTGGQTV.NPWI..GGVAT.VCQPNEFIMPD.AV.GDVLV
Retrocopy SQSMSEEEREKVTPLMVKGFRDAAEEGGTAVTGGQTVVNPWIIIGGVATVVCQPNEFIMPDSAVVGDVLV

Parental  LTKPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITG
          LTKPLGTQVAV..HQWLD.PE.W.KIK.VV..E.VELAYQEAM.NMA.LNRTAAGLMHTFNAHAATDITG
Retrocopy LTKPLGTQVAVNAHQWLDNPERWGKIKMVVSKEEVELAYQEAMFNMATLNRTAAGLMHTFNAHAATDITG

Parental  FGILGHAQNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCA
          FGILGH.QNLAKQQRNEVSFVIHNLP..AKMAAVSKA.G..FGL..GT..ETSGGLLICLPREQAARFC.
Retrocopy FGILGHSQNLAKQQRNEVSFVIHNLPIIAKMAAVSKASGR-FGLLQGTSSETSGGLLICLPREQAARFCS

Parental  EIKSPKYGEGHQAWIIGIVEKGNRTARIIDKPRIIEV
          EIKS.KYGEGHQAWI.GIVEKGNRTARIIDKPR.IEV
Retrocopy EIKSSKYGEGHQAWIVGIVEKGNRTARIIDKPRVIEV

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_792 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 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Dipodomys ordii	ENSDORG00000014119	1 retrocopy	retro_dord_792 ,
Equus caballus	ENSECAG00000014281	1 retrocopy	retro_ecab_77,
Homo sapiens	ENSG00000086475	3 retrocopies	retro_hsap_2196, retro_hsap_3860, retro_hsap_4705,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Mus musculus	ENSMUSG00000026662	1 retrocopy	retro_mmus_248,
Nomascus leucogenys	ENSNLEG00000012205	7 retrocopies	retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Otolemur garnettii	ENSOGAG00000007807	1 retrocopy	retro_ogar_3026,
Pan troglodytes	ENSPTRG00000002303	3 retrocopies	retro_ptro_1135, retro_ptro_1669, retro_ptro_3126,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,