RetrogeneDB ID: retro_dord_706

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_5920:17472..17817(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rplp2
• Ensembl ID: ENSDORG00000016458
• Aliases: None
• Description: ribosomal protein, large P2 [Source:MGI Symbol;Acc:MGI:1914436]

Sequence

>retro_dord_706
CTGCGCTGAGTCACCTCCGACCTTCTGGCAGCCCTTGGGGGCAACTCCTCCCCCATGTCCAAAGACATTAAGAAGATCCT
GGACAGCATGGGCATCCAGGTGGACGATGACCGGCTTCACAAGGTAATCAGTGAGCTGAATGGGAAGAACACTGAAGACA
TCATGGCCTAGGGTGTTGGCAAGCTTGCCAGTATGCCTGCTGGTGGGGCAGTTGTTGATTCTGCTGTGCCTGGCTCTGTA
GCACCTGTTGCTGGTTCTGCCCCTGCTGCAGCAAAAGAGAAGAAAGATGAGAAGAGAGAAGAATCCGAGGAGTCAGATGA
TGACATGGGATTTGCCCTCTTTGAT

Alignment

ORF - retro_dord_706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.91 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRYVASYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGVGKLASVPAGGA
          .R.V.S.LLAALGGNSSP..KDIKKILDS.GI..DDDRL.KVISELNGKN.ED..A.GVGKLAS.PAGGA
Retrocopy LR*VTSDLLAALGGNSSPMSKDIKKILDSMGIQVDDDRLHKVISELNGKNTEDIMA*GVGKLASMPAGGA

Parental  VVASAAPGSAAPAAGSAPAAAEEKKDEKKEESEESDDDMGFGLFD
          VV.SA.PGS.AP.AGSAPAAA..........SEESDDDMGF.LFD
Retrocopy VVDSAVPGSVAPVAGSAPAAAXXXXXXXXXXSEESDDDMGFALFD

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_706 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 16 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001777	2 retrocopies	retro_btau_117, retro_btau_1399,
Canis familiaris	ENSCAFG00000009523	1 retrocopy	retro_cfam_18,
Ciona intestinalis	ENSCING00000000626	1 retrocopy	retro_cint_34,
Dipodomys ordii	ENSDORG00000016458	3 retrocopies	retro_dord_705, retro_dord_706 , retro_dord_707,
Felis catus	ENSFCAG00000008417	1 retrocopy	retro_fcat_860,
Homo sapiens	ENSG00000177600	5 retrocopies	retro_hsap_1777, retro_hsap_3395, retro_hsap_3440, retro_hsap_821, retro_hsap_982,
Gorilla gorilla	ENSGGOG00000010789	5 retrocopies	retro_ggor_2238, retro_ggor_2298, retro_ggor_2323, retro_ggor_672, retro_ggor_784,
Macaca mulatta	ENSMMUG00000020627	2 retrocopies	retro_mmul_221, retro_mmul_311,
Mus musculus	ENSMUSG00000025508	4 retrocopies	retro_mmus_1364, retro_mmus_2111, retro_mmus_2282, retro_mmus_330,
Nomascus leucogenys	ENSNLEG00000026860	5 retrocopies	retro_nleu_1948, retro_nleu_2144, retro_nleu_2296, retro_nleu_2762, retro_nleu_85,
Otolemur garnettii	ENSOGAG00000016296	2 retrocopies	retro_ogar_156, retro_ogar_275,
Pongo abelii	ENSPPYG00000002885	6 retrocopies	retro_pabe_1537, retro_pabe_1543, retro_pabe_2789, retro_pabe_2844, retro_pabe_732, retro_pabe_830,
Pan troglodytes	ENSPTRG00000003137	5 retrocopies	retro_ptro_1189, retro_ptro_2307, retro_ptro_2332, retro_ptro_572, retro_ptro_764,
Rattus norvegicus	ENSRNOG00000002116	3 retrocopies	retro_rnor_257, retro_rnor_320, retro_rnor_388,
Sarcophilus harrisii	ENSSHAG00000001056	1 retrocopy	retro_shar_321,
Sus scrofa	ENSSSCG00000012842	1 retrocopy	retro_sscr_54,