RetrogeneDB ID: retro_dord_202

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_5350:62518..62921(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Anapc10
• Ensembl ID: ENSDORG00000016690
• Aliases: None
• Description: anaphase promoting complex subunit 10 [Source:MGI Symbol;Acc:MGI:1916249]

Sequence

>retro_dord_202
CCAGGTTTTGGAGTGGATCAATTACAAGACGGCAACCTAGAAACAAACTGGCAATCTGATGGCTCCCAGCCACATTTAGT
GAACATCCAATTCAGAAGAAAAACAACAGTAAAGACATTGTGTATTTATGAACACTATAAACCTGATGAAAGCTACACTC
CAAGCAAAATCTCAGTCAGAGTAGGAAATAATTTTCACAACCTTCAAGAAATTCGACAACTTGAATTGGTGGAACCAAGT
GGCTTGATTCATGTTTCCCCTAACTGACAGGCATAAGAAGCCAACTCGAACATTCATGATACAGATTGTTGTCCTAGCCA
ATCACCAAAATGGAAGAGACACCCACATGAGACAAATTAAAATATACACACCAGTGCAAGAAACTTTAATTGGTAAATTA
CCT

Alignment

ORF - retro_dord_202 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 72.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PGFGVDQLRDDNLETYWQSDGSQPHLVNIQFRRKTTVKTLCIYADYKSDESYTPSKISVRVGNNFHNLQE
          PGFGVDQL.D.NLET.WQSDGSQPHLVNIQFRRKTTVKTLCIY..YK.DESYTPSKISVRVGNNFHNLQE
Retrocopy PGFGVDQLQDGNLETNWQSDGSQPHLVNIQFRRKTTVKTLCIYEHYKPDESYTPSKISVRVGNNFHNLQE

Parental  IRQLELVEPSGWIHV-PLTDNLKKPTRTFMIQIAVLANHQNGRDTHMRQIKIYTPVEESSIGKFP
          IRQLELVEPSG.IHV.PLTD..KKPTRTFMIQI.VLANHQNGRDTHMRQIKIYTPV.E..IGK.P
Retrocopy IRQLELVEPSGLIHV>PLTDRHKKPTRTFMIQIVVLANHQNGRDTHMRQIKIYTPVQETLIGKLP

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_202 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002663	2 retrocopies	retro_cjac_2683, retro_cjac_2999,
Dipodomys ordii	ENSDORG00000016690	1 retrocopy	retro_dord_202 ,
Homo sapiens	ENSG00000164162	1 retrocopy	retro_hsap_152,
Gorilla gorilla	ENSGGOG00000025091	1 retrocopy	retro_ggor_241,
Myotis lucifugus	ENSMLUG00000008607	1 retrocopy	retro_mluc_1679,
Macaca mulatta	ENSMMUG00000004432	1 retrocopy	retro_mmul_374,
Mus musculus	ENSMUSG00000036977	1 retrocopy	retro_mmus_1511,
Nomascus leucogenys	ENSNLEG00000005453	1 retrocopy	retro_nleu_1498,
Otolemur garnettii	ENSOGAG00000006902	2 retrocopies	retro_ogar_1649, retro_ogar_2510,
Pongo abelii	ENSPPYG00000015096	1 retrocopy	retro_pabe_468,
Pan troglodytes	ENSPTRG00000016480	1 retrocopy	retro_ptro_149,
Pteropus vampyrus	ENSPVAG00000013169	2 retrocopies	retro_pvam_1245, retro_pvam_1450,