RetrogeneDB ID: retro_dord_292

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_10247:38389..38911(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Chmp5
• Ensembl ID: ENSDORG00000006280
• Aliases: None
• Description: charged multivesicular body protein 5 [Source:MGI Symbol;Acc:MGI:1924209]

Sequence

>retro_dord_292
AAGGATCAAATCAAAAAGATGAGAGAGGGTTCTGCCAAGACCACAGTGAAGAAGAAAGCCCCATGGGTTTTTAAAGCAAA
GGCGAATGTTTGAGCATCAGCAGGATACCCTTGCCCAACAGTTTTCAACATGAACAAGCCAATTATACCATCCAGTCATT
AAAAGACACCAAGACCACGATGGATGCAAAGAAGCTAGGAGTAAAGGAAATGAAAGAAGACATATAAGCAAGTGAAAATC
AACCAGACTGAGAATTTACAAGACCAGCTGGAAGATACAATGGAAGATGCAAATAAAATCAAAGGAGCACTAAGTCGAAG
TTATGGCACCCCAGAATTAGATGAAGATGACCTAGAAGCAGAGTTGGATGCATTCAGTGATGAGCTTCTGGCTGATGAAG
GTAGTTCTTCCTTGGATGAAGCAGCATCTGCACCTGCCATTTCAGGAGGTGTTCCCGCTGACACAAAAAACAAGGATGGA
GTCCTGGTGGATGAATCTGGATTGCCACAGATCTCTGCTTCA

Alignment

ORF - retro_dord_292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.34 %
• Parental protein coverage: 79.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KDQIKKMREGPAKNMVKQKALRV-LKQKRMYEQQRDNLAQQS-FNM-EQANYTIQSLKDTKTTVDAMKLG
          KDQIKKMREG.AK..VK.KA..V.LKQ.RM.E.Q.D.LAQQ..FNM.EQANYTIQSLKDTKTT.DA.KLG
Retrocopy KDQIKKMREGSAKTTVKKKAPWV>LKQRRMFEHQQDTLAQQF<FNM<EQANYTIQSLKDTKTTMDAKKLG

Parental  VKEM-KKAYKQVKIDQIEDLQDQLEDMMEDANEIQEALSRSYGTPELDEDDLEAELDALGDELLADEDSS
          VKEM.KK.YKQVKI.Q.E.LQDQLED.MEDAN.I..ALSRSYGTPELDEDDLEAELDA..DELLADE.SS
Retrocopy VKEM>KKTYKQVKINQTENLQDQLEDTMEDANKIKGALSRSYGTPELDEDDLEAELDAFSDELLADEGSS

Parental  YLDEAASAPAIPEGVPTDTKNKDGVLVDEFGLPQIPAS
          .LDEAASAPAI..GVP.DTKNKDGVLVDE.GLPQI.AS
Retrocopy SLDEAASAPAISGGVPADTKNKDGVLVDESGLPQISAS

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_292 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 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012672	1 retrocopy	retro_chof_2045,
Callithrix jacchus	ENSCJAG00000008104	2 retrocopies	retro_cjac_2868, retro_cjac_4159,
Cavia porcellus	ENSCPOG00000003467	2 retrocopies	retro_cpor_1221, retro_cpor_1306,
Dipodomys ordii	ENSDORG00000006280	2 retrocopies	retro_dord_292 , retro_dord_764,
Echinops telfairi	ENSETEG00000001424	1 retrocopy	retro_etel_2126,
Homo sapiens	ENSG00000086065	2 retrocopies	retro_hsap_4822, retro_hsap_494,
Microcebus murinus	ENSMICG00000012113	2 retrocopies	retro_mmur_369, retro_mmur_843,
Myotis lucifugus	ENSMLUG00000011045	1 retrocopy	retro_mluc_954,
Macaca mulatta	ENSMMUG00000020149	1 retrocopy	retro_mmul_2573,
Monodelphis domestica	ENSMODG00000004012	2 retrocopies	retro_mdom_2002, retro_mdom_595,
Mus musculus	ENSMUSG00000028419	1 retrocopy	retro_mmus_1469,
Nomascus leucogenys	ENSNLEG00000005158	2 retrocopies	retro_nleu_2197, retro_nleu_2420,
Otolemur garnettii	ENSOGAG00000000774	6 retrocopies	retro_ogar_2072, retro_ogar_2190, retro_ogar_2386, retro_ogar_2504, retro_ogar_2509, retro_ogar_916,
Pongo abelii	ENSPPYG00000019137	2 retrocopies	retro_pabe_239, retro_pabe_3750,
Pan troglodytes	ENSPTRG00000020857	2 retrocopies	retro_ptro_3210, retro_ptro_373,
Rattus norvegicus	ENSRNOG00000008672	1 retrocopy	retro_rnor_2614,
Ictidomys tridecemlineatus	ENSSTOG00000026573	1 retrocopy	retro_itri_424,
Tupaia belangeri	ENSTBEG00000003486	5 retrocopies	retro_tbel_1626, retro_tbel_1894, retro_tbel_2407, retro_tbel_3364, retro_tbel_3494,
Tursiops truncatus	ENSTTRG00000010575	1 retrocopy	retro_ttru_338,