RetrogeneDB ID: retro_dord_118

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_36:14128..14524(-)
• Located in intron of: ENSDORG00000006173

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrps15
• Ensembl ID: ENSDORG00000007581
• Aliases: None
• Description: mitochondrial ribosomal protein S15 [Source:MGI Symbol;Acc:MGI:1913657]

Sequence

>retro_dord_118
TTGAGAAGGCTTCTCGTTTTTAGAAATGGCCAACTTGAAAGCAAGGTAAAAGTCAAGCAAGAACAGCTGATGAAACAGGG
TCATGGCAAACCCAGAGGATACCAGACACCTAGAGGCTCAAGTTGTTGCTTCAACCCTCAATACCTGCAATTATGAAGAA
CACATTCAAAAATATAGAAAGGACAAAGCCCACAAATGCTCTCTTCTGATAAACATGGGCCAGAGGAAGAAGATGCTTCA
TAAGACCAAATATGATGTCTTTGAGAAGATATGCAGGGAGTGATGGGTTCAGTACACCTTTCCCCTTCTACAGGACAGAA
AGCCCACTGCTGATTCGTGACCAAGAAGGCTCTGTGCATCTGGGTTTTCCAGCAGCAACAAAAGCTTAAGGAGCAA

Alignment

ORF - retro_dord_118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.09 %
• Parental protein coverage: 53.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VKRVLSLEMASKKEKLKVKQEQLM-NKIMANLEDTRSLEARIVSLTVKIRSLEEHMQKHQKDKAQKRHLL
          ..R.L.........K.KVKQEQLM.N..MAN.EDTR.LEA..V..T......EEH.QK..KDKA.K..LL
Retrocopy LRRLLVFRNGQLESKVKVKQEQLM>NRVMANPEDTRHLEAQVVASTLNTCNYEEHIQKYRKDKAHKCSLL

Parental  MSTAKRKKMLKNLRKINYDVFEKICKELGIEYT-ITPLYCRKAHRRLLIKKALCLRVFQEKQKLKKQ
          .....RKKML....K..YDVFEKIC.E....YT...P....KAH.....KKALC..VFQ..QKLK.Q
Retrocopy INMGQRKKML---HKTKYDVFEKICRE*WVQYT<LSPSTGQKAHC*FVTKKALCIWVFQQQQKLKEQ

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_118 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 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001463	1 retrocopy	retro_amel_1564,
Canis familiaris	ENSCAFG00000030390	1 retrocopy	retro_cfam_1939,
Callithrix jacchus	ENSCJAG00000001852	3 retrocopies	retro_cjac_3095, retro_cjac_761, retro_cjac_859,
Cavia porcellus	ENSCPOG00000010877	1 retrocopy	retro_cpor_430,
Dipodomys ordii	ENSDORG00000007581	1 retrocopy	retro_dord_118 ,
Felis catus	ENSFCAG00000005265	1 retrocopy	retro_fcat_915,
Homo sapiens	ENSG00000116898	1 retrocopy	retro_hsap_1594,
Myotis lucifugus	ENSMLUG00000006475	1 retrocopy	retro_mluc_1945,
Monodelphis domestica	ENSMODG00000017813	1 retrocopy	retro_mdom_1094,
Mus musculus	ENSMUSG00000028861	1 retrocopy	retro_mmus_3447,
Nomascus leucogenys	ENSNLEG00000011467	1 retrocopy	retro_nleu_615,
Otolemur garnettii	ENSOGAG00000002656	2 retrocopies	retro_ogar_1327, retro_ogar_16,
Pongo abelii	ENSPPYG00000001537	1 retrocopy	retro_pabe_1310,
Pan troglodytes	ENSPTRG00000000541	1 retrocopy	retro_ptro_1071,
Sus scrofa	ENSSSCG00000026393	1 retrocopy	retro_sscr_1190,
Ictidomys tridecemlineatus	ENSSTOG00000000608	1 retrocopy	retro_itri_454,
Tupaia belangeri	ENSTBEG00000000958	4 retrocopies	retro_tbel_1633, retro_tbel_4438, retro_tbel_845, retro_tbel_882,
Tarsius syrichta	ENSTSYG00000008948	2 retrocopies	retro_tsyr_1612, retro_tsyr_372,
Tursiops truncatus	ENSTTRG00000002345	1 retrocopy	retro_ttru_1500,