RetrogeneDB ID: retro_dord_277

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_6862:493085..493869(+)
• Located in intron of: ENSDORG00000003341

Retrocopy information

• Ensembl ID: ENSDORG00000003344
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rnf167
• Ensembl ID: ENSDORG00000011757
• Aliases: None
• Description: ring finger protein 167 [Source:MGI Symbol;Acc:MGI:1917760]

Sequence

>retro_dord_277
GACTGCAACTTTGACCTCAAGGTCCTAAATGCACAGAAAGCTGGATATGGCGCAGCAGTGGTACACAATGTAAATTCCAA
CGAACTTCTCAACATGGTGTGGAACAGTGAGGAAATCCAGCAGCAGATCTGGATTCCATCTGTCTTTATTGGAGAAAGAA
GTGCTGAGTACTTGCGTGCCCTCTTTGTCTACGAGAAGGGGGCTCGGGTACTTCTGGTTCCAGACAATAGCTTCCCTCTT
GGCTATTACCTCATTCCTTTCACTGGGATAGTAGGACTGCTGGTTTTGGCCATGGGAACAGTAATGATAGTGCGTTGTAT
CCAACACCGGAAACGGCTTCAACGGAATCGGCTTACCAAAGAGCAATTGAAACAGATTCCTACCCATGACTATCAAAAGG
GAGACCAGTATGATGTTTGTGCCATCTGCTTGGATGAATATGAAGACGGGGACAAGCTGCGTGTACTCCCCTGTGCTCAT
GCCTATCACAGCCGCTGTGTGGACCCCTGGCTTACTCAAACCCGGAAGACTTGCCCCATCTGCAAGCAGCCAGTTCATTG
GGGCCCTGGGGATGAGGAGCAGAAATCAAGGCCATGAGGAGGGTGATGAGGAAGGGGAGCCAAGGTACCACCCTGCCTCA
GAGCGAACCCCACTCCTGGGCTCCAGTCCCACCCTCCCTGCCTCCTTTGGCTCTCTAGCCCCAGCGCCTTTGGTTTTTCC
TGGGCCATCAACAGAACCCCCACCTTCTCCTTCTTTCTCCTCTCCCTCATCTGCCATTCTAGCC

Alignment

ORF - retro_dord_277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.96 %
• Parental protein coverage: 74.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DCNFD-KVLNAQKAGYGAAVVHNVNSNELLNMVWNSEEIQQQIWIPSVFIGERSAEYLRALFVYEKGARV
          DCNFD.KVLNAQKAGYGAAVVHNVNSNELLNMVWNSEEIQQQIWIPSVFIGERSAEYLRALFVYEKGARV
Retrocopy DCNFDLKVLNAQKAGYGAAVVHNVNSNELLNMVWNSEEIQQQIWIPSVFIGERSAEYLRALFVYEKGARV

Parental  LLVPDNSFPLGYYLIPFTGIVGLLVLAMGTVMIVRCIQHRKRLQRNRLTKEQLKQIPTHDYQKGDQYDVC
          LLVPDNSFPLGYYLIPFTGIVGLLVLAMGTVMIVRCIQHRKRLQRNRLTKEQLKQIPTHDYQKGDQYDVC
Retrocopy LLVPDNSFPLGYYLIPFTGIVGLLVLAMGTVMIVRCIQHRKRLQRNRLTKEQLKQIPTHDYQKGDQYDVC

Parental  AICLDEYEDGDKLRVLPCAHAYHSRCVDPWLTQTRKTCPICKQPVHRGPGPGDEE-NQGHEEGDEEGEPR
          AICLDEYEDGDKLRVLPCAHAYHSRCVDPWLTQTRKTCPICKQPVH.GPG...E..NQGHEEGDEEGEPR
Retrocopy AICLDEYEDGDKLRVLPCAHAYHSRCVDPWLTQTRKTCPICKQPVHWGPGD-EEQ>NQGHEEGDEEGEPR

Parental  DHPASERTPLLGSSPTLPASFGSLAPAPLVFPGPSTEPPPSPSFSSPSSAILA
          .HPASERTPLLGSSPTLPASFGSLAPAPLVFPGPSTEPPPSPSFSSPSSAILA
Retrocopy YHPASERTPLLGSSPTLPASFGSLAPAPLVFPGPSTEPPPSPSFSSPSSAILA

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_277 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006392	1 retrocopy	retro_amel_43,
Bos taurus	ENSBTAG00000004913	1 retrocopy	retro_btau_217,
Canis familiaris	ENSCAFG00000015830	2 retrocopies	retro_cfam_1053, retro_cfam_84,
Dipodomys ordii	ENSDORG00000011757	2 retrocopies	retro_dord_277 , retro_dord_432,
Equus caballus	ENSECAG00000021567	1 retrocopy	retro_ecab_583,
Felis catus	ENSFCAG00000011173	1 retrocopy	retro_fcat_99,
Mustela putorius furo	ENSMPUG00000010940	1 retrocopy	retro_mputfur_95,
Pteropus vampyrus	ENSPVAG00000003781	1 retrocopy	retro_pvam_1206,
Sorex araneus	ENSSARG00000011216	1 retrocopy	retro_sara_517,
Sus scrofa	ENSSSCG00000017906	1 retrocopy	retro_sscr_518,
Tursiops truncatus	ENSTTRG00000001298	1 retrocopy	retro_ttru_1062,