RetrogeneDB ID: retro_dord_67

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_1936:92979..93519(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BC023829
• Ensembl ID: ENSDORG00000015027
• Aliases: None
• Description: cDNA sequence BC023829 [Source:MGI Symbol;Acc:MGI:2448555]

Sequence

>retro_dord_67
GTGGTGTTTGTGCCCTTGTGGATCCTCATGTCCTTCCTCTGCCTGGTGGTGCTCTACTATGTCGTGTGGTCCCTCCTGTT
CCTGCGGTCGCTGGATGTGGTGGCTGAACAGCGCAGAACACACGTGACCATGGCCGTCAGCTGGATAACCATTGTCGTGC
CCCTGCTCACATTCGAGGTCCTGCTGGTTCACAGGTTGGATGGCCACAATACGTTCTCTTACATTTCCATCTTCGTTCCT
CTTTGGCTCTCCTTAATAACTTTGATGGCTACAACATTTAGGCGAAAAGGAGGCAATCATTGGTGGTTTGGTATTCGCCG
AGACTTCTGTCAGTTTCTGCTGGAGATTTTCCCCTTTTTAAGAGAATACGGGAATATTTCTTATGATCTCCATCATGAAG
ACAGTGAAGATGCTGAAGAAACAGGTTCTGAAGCACCAAAAATCGCTCCAGTGTTTGGAAAGAAAGCCAGGGTAGTTATA
ACTCAGAGCCCTGGGAAATACGTTCCTCCACCCCCCAAGTTAAATATCGATATGCCAGAC

Alignment

ORF - retro_dord_67 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.08 %
• Parental protein coverage: 52.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTHITMALSWMTIVVPLLTFEILLVHKLDGHN
          VV.VPLWILMSFLCLVVLYY.VWS.LFLRS.DV.AEQRRTH.TMA.SW.TIVVPLLTFE.LLVH.LDGHN
Retrocopy VVFVPLWILMSFLCLVVLYYVVWSLLFLRSLDVVAEQRRTHVTMAVSWITIVVPLLTFEVLLVHRLDGHN

Parental  AFSCIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQFLLEIFPFLREYGNISYDLHHEDNEEMEE
          .FS.I.IFVPLWLSLITLMATTF..KGGNHWWFGIR.DFCQFLLEIFPFLREYGNISYDLHHED.E..EE
Retrocopy TFSYISIFVPLWLSLITLMATTFRRKGGNHWWFGIRRDFCQFLLEIFPFLREYGNISYDLHHEDSEDAEE

Parental  TPVPEPPKIAPMFRKKARVVITQSPGKYVLPPPKLNIEMPD
          T...E.PKIAP.F.KKARVVITQSPGKYV.PPPKLNI.MPD
Retrocopy TG-SEAPKIAPVFGKKARVVITQSPGKYVPPPPKLNIDMPD

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_67 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 26 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008637	1 retrocopy	retro_acar_65,
Ailuropoda melanoleuca	ENSAMEG00000009351	1 retrocopy	retro_amel_8,
Bos taurus	ENSBTAG00000006818	1 retrocopy	retro_btau_1,
Canis familiaris	ENSCAFG00000019103	1 retrocopy	retro_cfam_159,
Cavia porcellus	ENSCPOG00000003622	1 retrocopy	retro_cpor_5,
Dasypus novemcinctus	ENSDNOG00000011864	1 retrocopy	retro_dnov_2451,
Dipodomys ordii	ENSDORG00000015027	1 retrocopy	retro_dord_67 ,
Equus caballus	ENSECAG00000009399	1 retrocopy	retro_ecab_426,
Felis catus	ENSFCAG00000024483	1 retrocopy	retro_fcat_1116,
Homo sapiens	ENSG00000155984	1 retrocopy	retro_hsap_104,
Gorilla gorilla	ENSGGOG00000024268	1 retrocopy	retro_ggor_189,
Loxodonta africana	ENSLAFG00000003044	1 retrocopy	retro_lafr_898,
Microcebus murinus	ENSMICG00000004639	1 retrocopy	retro_mmur_106,
Myotis lucifugus	ENSMLUG00000001319	1 retrocopy	retro_mluc_2075,
Macaca mulatta	ENSMMUG00000002888	1 retrocopy	retro_mmul_310,
Mustela putorius furo	ENSMPUG00000011896	1 retrocopy	retro_mputfur_46,
Mus musculus	ENSMUSG00000073139	1 retrocopy	retro_mmus_358,
Nomascus leucogenys	ENSNLEG00000013487	1 retrocopy	retro_nleu_2723,
Otolemur garnettii	ENSOGAG00000016414	1 retrocopy	retro_ogar_88,
Procavia capensis	ENSPCAG00000009160	1 retrocopy	retro_pcap_260,
Pongo abelii	ENSPPYG00000020809	1 retrocopy	retro_pabe_118,
Pteropus vampyrus	ENSPVAG00000013822	1 retrocopy	retro_pvam_30,
Rattus norvegicus	ENSRNOG00000011047	1 retrocopy	retro_rnor_6,
Sus scrofa	ENSSSCG00000012739	1 retrocopy	retro_sscr_494,
Ictidomys tridecemlineatus	ENSSTOG00000014484	1 retrocopy	retro_itri_8,
Tursiops truncatus	ENSTTRG00000000643	1 retrocopy	retro_ttru_868,