RetrogeneDB ID: retro_dord_339

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_128160:495..990(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Atpbd4
• Ensembl ID: ENSDORG00000012219
• Aliases: None
• Description: ATP binding domain 4 [Source:MGI Symbol;Acc:MGI:1913882]

Sequence

>retro_dord_339
CTTTTGAAACTTGTCAAGGAAAAAGAAGTAGAGGGGATATCAGGAGGAGCCATACTTTCTGATTATCAGCGTGTTCAAGT
AGAAAATGGATGCAAAAGGCTAAGTCTTCAGCCTTTGGCTTACCTTTGGCAGAGGAGCCAGGAGGACTTGCTCCCAGAGA
TGATCGAATCTGATATTCAAGCCGTGATCTTCACAGTGGCAGCTTTGGGTTTGGATCCAGATAAGCATCTTGGTAAAACC
CTGAATGAAATGGAGCCTTATCTCTTAGAGCTTTCTAAGAAGTATGGAGTTCATGTATGTGGAGAAGTTGGAGAATATGA
GACGTTCACTTTGGACTGCCCTCTATTTAGGAAGAAAATAATTGTGGACTCCTGGGAAGTAGTCGTCCATTCGGCTGATG
CATTTGCACCTGTGGTCTATCTACGCTTTTTAGAGGCGCACTTGGAAGACAAGGTGTTTCCTGTTCCTGACAAAACATCC
AGTGATAGACATGAT

Alignment

ORF - retro_dord_339 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.69 %
• Parental protein coverage: 63.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLKLVKEKEDVEGISVGAILSDYQRVRVENVCKRLSLQPLAYLWQRNQEDLLREMIESDIQAVIIKVAAL
          LLKLVKEKE.VEGIS.GAILSDYQRV.VEN.CKRLSLQPLAYLWQR.QEDLL.EMIESDIQAVI..VAAL
Retrocopy LLKLVKEKE-VEGISGGAILSDYQRVQVENGCKRLSLQPLAYLWQRSQEDLLPEMIESDIQAVIFTVAAL

Parental  GLDPDKHLGKTLTEMEPYLLELSKKYGVHVCGEGGEYETFTLDCPLFKKKIIVDSWEVVVHSDDAFAPVA
          GLDPDKHLGKTL.EMEPYLLELSKKYGVHVCGE.GEYETFTLDCPLF.KKIIVDSWEVVVHS.DAFAPV.
Retrocopy GLDPDKHLGKTLNEMEPYLLELSKKYGVHVCGEVGEYETFTLDCPLFRKKIIVDSWEVVVHSADAFAPVV

Parental  YLRFLEAHLEDKVFPGPDNYRTSNDRHN
          YLRFLEAHLEDKVFP.PD...TS.DRH.
Retrocopy YLRFLEAHLEDKVFPVPD--KTSSDRHD

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_339 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000012219	1 retrocopy	retro_dord_339 ,
Myotis lucifugus	ENSMLUG00000010097	1 retrocopy	retro_mluc_2438,