RetrogeneDB ID: retro_dord_547

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_29855:6664..7021(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rbm3
• Ensembl ID: ENSDORG00000000182
• Aliases: None
• Description: RNA binding motif protein 3 [Source:MGI Symbol;Acc:MGI:1099460]

Sequence

>retro_dord_547
ATGTCTTCTGAAGAAGGCAAACTCTTCGTGGGAGGACTGAACTTTAACACTGATAAGCAGGTACTTGAAGACCACTTCAG
CAGCTTCAGGCCTATTTTTGAAGTGGTTGTTGTCAAGAAATGCGAGACTCAACGATCCTGACGTTTTGGCTTCATCACCT
TCACCAACCCAGAATATGCCTCAGATGCCATGAATGGAGAGTCTCTAAATGGTCGATAGATCTGAATGGACCATGCAGGC
AAGTCTGCCTGGGGCACAAGAAGGGGGTACCTTTGAGAACCATGGAGTGATCACAGCTACTCTGGAGGTGGCAGGGACCA
GAGATATGGGAGTGGCAGGTATGACAGTTGGCCTGGA

Alignment

ORF - retro_dord_547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.0 %
• Parental protein coverage: 78.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSEEGKLFVGGLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASDAMRAMNGE
          MSSEEGKLFVGGLNFNTD.Q.LEDHFSSF.PI.EVVVVK..ETQRS..FGFITFTNPE.ASDAM...NGE
Retrocopy MSSEEGKLFVGGLNFNTDKQVLEDHFSSFRPIFEVVVVKKCETQRS*RFGFITFTNPEYASDAM---NGE

Parental  SLDGRQIRVDHAGKSARGTR-GGGAFGGHG-RGRSYSRGGGDQGYGSGRYDSRPG
          SL.GR.I..DHAGKSA.GTR.GG..F..HG....SYS.GG.DQ.YGSGRYDS.PG
Retrocopy SLNGR*I*MDHAGKSAWGTR>GG-TFENHG<SDHSYSGGGRDQRYGSGRYDSWPG

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_547 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 20 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013718	1 retrocopy	retro_acar_197,
Ailuropoda melanoleuca	ENSAMEG00000012653	1 retrocopy	retro_amel_519,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Canis familiaris	ENSCAFG00000015485	2 retrocopies	retro_cfam_1475, retro_cfam_259,
Dipodomys ordii	ENSDORG00000000182	1 retrocopy	retro_dord_547 ,
Dipodomys ordii	ENSDORG00000015481	1 retrocopy	retro_dord_793,
Equus caballus	ENSECAG00000024257	2 retrocopies	retro_ecab_130, retro_ecab_589,
Homo sapiens	ENSG00000102317	1 retrocopy	retro_hsap_265,
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Loxodonta africana	ENSLAFG00000007003	1 retrocopy	retro_lafr_1091,
Myotis lucifugus	ENSMLUG00000003996	1 retrocopy	retro_mluc_1013,
Mus musculus	ENSMUSG00000031167	4 retrocopies	retro_mmus_2044, retro_mmus_2963, retro_mmus_3019, retro_mmus_501,
Nomascus leucogenys	ENSNLEG00000007841	2 retrocopies	retro_nleu_2591, retro_nleu_867,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Pan troglodytes	ENSPTRG00000021864	1 retrocopy	retro_ptro_222,
Pteropus vampyrus	ENSPVAG00000015630	1 retrocopy	retro_pvam_953,
Sus scrofa	ENSSSCG00000021591	1 retrocopy	retro_sscr_842,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142,
Tarsius syrichta	ENSTSYG00000008670	4 retrocopies	retro_tsyr_1733, retro_tsyr_197, retro_tsyr_2002, retro_tsyr_679,
Tursiops truncatus	ENSTTRG00000008587	3 retrocopies	retro_ttru_1898, retro_ttru_928, retro_ttru_938,