RetrogeneDB ID: retro_dord_698

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_58002:1281..1955(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ostf1
• Ensembl ID: ENSDORG00000002933
• Aliases: None
• Description: osteoclast stimulating factor 1 [Source:MGI Symbol;Acc:MGI:700012]

Sequence

>retro_dord_698
ATATGTGCCTGGTCTCAAGCAGCTGCTCAAGGAAGCGAGATGTCGAGGCTGCTTCCCAAACGAGTCAAACAAAGACAAGT
TAAAGTCTTCAGGGCTCTATATACTTTTGAACCCAGAACTCCAGATGAACTGTACTTTGAAGAAGGTGATATTATCTATA
TGACTGACATGAGTGATGCCAATTGATGGAAAAGGACCTGCAAATGCAAGACGGGGCTCATTCCGAGCAATTACATGGCT
GAGCGGGCAGAATCCATTGCCAATCCATTGCCTGAAACTGCAGAAAGAGGCAACCTGAGCTGGCTGAGAGAGTGCTTGGA
CAACTGAGTGGGCGTGAACGGCTTAGACAAAGCTGGAAGCACAGTCTTGTACTGCCACAGGGGTCACGAAGACGTGGTGG
AAGCTCTATTTATTCAGCCCCATATTGAACTGAACCAGAGAACAAGTTGGGGGACACAACTTTGCATACTGCTGCCTGGA
AGGGCTATGCTGACATTGTCCAGTTACTTTTGGCAAAAGGTGCGAGAACAGACTTAAGAAACAATGAGAAGAAGCTGGCT
TTGGACATGGCCATGAATGCTGACTGTGCGTCTTTCCTGAAAAAGAATCAGGGAACAGATAAAGTTTGAACATTAAGCAA
TAGAGACGACTATCTTGATGATAAAGAGTCAGAT

Alignment

ORF - retro_dord_698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.07 %
• Parental protein coverage: 85.98 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ISLFPRCAAPGSAMSKPPPKPVKPGQVKVFRALYTFEPRTPDELYFEEGDIIYITDMSDTNWWKGTCKGR
          I......AA.GS.MS...PK.VK..QVKVFRALYTFEPRTPDELYFEEGDIIY.TDMSD.N.WK.TCK..
Retrocopy ICAWSQAAAQGSEMSRLLPKRVKQRQVKVFRALYTFEPRTPDELYFEEGDIIYMTDMSDAN*WKRTCKCK

Parental  TGLIPSNYVAEQAESIDNPLHEAAKRGNLSWLRECLDNRVGVNGLDKAGSTALYWACHGGHKDVVEVLFT
          TGLIPSNY.AE.AESI.NPL.E.A.RGNLSWLRECLDN.VGVNGLDKAGST.LY..CH.GH.DVVE.LF.
Retrocopy TGLIPSNYMAERAESIANPLPETAERGNLSWLRECLDN*VGVNGLDKAGSTVLY--CHRGHEDVVEALFI

Parental  QSNIELNQ-QNKLGDTALHAAAWKGYADIVQLLLAKGARTDLRNNEKKLALDMATNAACASLLKKKQGTD
          Q..IELNQ..NKLGDT.LH.AAWKGYADIVQLLLAKGARTDLRNNEKKLALDMA.NA.CAS.LKK.QGTD
Retrocopy QPHIELNQ<ENKLGDTTLHTAAWKGYADIVQLLLAKGARTDLRNNEKKLALDMAMNADCASFLKKNQGTD

Parental  AVRTLSNAEDYLDDEDSD
          .V.TLSN..DYLDD..SD
Retrocopy KV*TLSNRDDYLDDKESD

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_698 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 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012808	1 retrocopy	retro_cjac_3249,
Cavia porcellus	ENSCPOG00000007226	1 retrocopy	retro_cpor_1049,
Dipodomys ordii	ENSDORG00000002933	1 retrocopy	retro_dord_698 ,
Erinaceus europaeus	ENSEEUG00000008320	2 retrocopies	retro_eeur_545, retro_eeur_683,
Felis catus	ENSFCAG00000022374	1 retrocopy	retro_fcat_1869,
Homo sapiens	ENSG00000134996	1 retrocopy	retro_hsap_1058,
Gorilla gorilla	ENSGGOG00000011920	1 retrocopy	retro_ggor_836,
Macaca mulatta	ENSMMUG00000010401	1 retrocopy	retro_mmul_836,
Nomascus leucogenys	ENSNLEG00000001854	1 retrocopy	retro_nleu_2502,
Otolemur garnettii	ENSOGAG00000002603	1 retrocopy	retro_ogar_2962,
Pongo abelii	ENSPPYG00000019300	1 retrocopy	retro_pabe_883,
Pan troglodytes	ENSPTRG00000021031	1 retrocopy	retro_ptro_720,
Rattus norvegicus	ENSRNOG00000012156	2 retrocopies	retro_rnor_936, retro_rnor_937,
Sus scrofa	ENSSSCG00000005273	1 retrocopy	retro_sscr_979,
Tursiops truncatus	ENSTTRG00000003081	1 retrocopy	retro_ttru_492,