RetrogeneDB ID: retro_dord_389

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_15580:12388..13086(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl16
• Ensembl ID: ENSDORG00000015111
• Aliases: None
• Description: mitochondrial ribosomal protein L16 [Source:MGI Symbol;Acc:MGI:2137219]

Sequence

>retro_dord_389
ACAGCCGCTCCCGCCAGTGTGGGCTCAAGATGCTACTTCCAGTGCCATGTTTTGAAGATGTTTCTATTCCTGATAAACCC
AAGCTTAAATCTGTTGAAAGGACACCCCTTGTCCCAAAAGTAAAAAAAGAACCTAAAAACTTGAAAGACATTTGGGGCCC
TTCCACCGAAGCTACTGACTTCACAGAAGGCAATTTTGCAATTTTGGCATTGGGAGGTGGTTACTTCCATTGGGGCCATT
TTGAAATGATGTGCCTGACAATCAACCTCTCTATGGACCCAAAGAACATGTTTGCTCGCTAGAGAATTCCAGCCCCTTTC
AAGCCTATCACCCGCAAAGGTGTCGGGCAGCACATGGGTGGGAGGCAAAGGCGCGATCGATCACTATGTGACCCCCGTGA
AGGCTGGCCGCCTCATAGTAGAGATGGGGGGGGGAGGTGGTGCTGTGAATTCAAAGAAGTACAGGGTTTCTTGGAGCAGG
TTGCCCACAAGTTGCCTTTCCCAGTGAAGGCTGTGAGTCGCGAGACTCTGGACAAGATGCGAGAACTTCAAGAGGAAAGA
GAAGGAAACAACCAAAACCCCTGGACCTTTGAGCGTATAGTCACCGCCAACATGCTGGGCATCTGGAAGGTGTTAAGCCC
GTATGACTTGACCCAAAAGGGCCGATACTGGGGCAAGTTCTACTTGCCTGAACGCATG

Alignment

ORF - retro_dord_389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.59 %
• Parental protein coverage: 91.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TATPASAG-LKTLLPVPTFEDVSIPDKPKLKFVERAPLVPKVRREPKNLKDIRGPSTEATEFTEGNFAIL
          TA.PAS.G.LK.LLPVP.FEDVSIPDKPKLK.VER.PLVPKV..EPKNLKDI.GPSTEAT.FTEGNFAIL
Retrocopy TAAPASVG<LKMLLPVPCFEDVSIPDKPKLKSVERTPLVPKVKKEPKNLKDIWGPSTEATDFTEGNFAIL

Parental  ALGGGYLHWGHFEMMRLTINRSMDPKNMFALWRVPAPFKPITRKGVGQRMG-GGKGAIDHYVTPVKAGRL
          ALGGGY.HWGHFEMM.LTIN.SMDPKNMFA..R.PAPFKPITRKGVGQ.MG.GGKGAIDHYVTPVKAGRL
Retrocopy ALGGGYFHWGHFEMMCLTINLSMDPKNMFAR*RIPAPFKPITRKGVGQHMG>GGKGAIDHYVTPVKAGRL

Parental  IVE---MGGRCEFK-EVQGFLEQVAHKLPFPAKAVSRETLEKMRELQEEKERNNQNPWTFERIVTANMLG
          IVE....GG....K.EVQGFLEQVAHKLPFP.KAVSRETL.KMRELQEE.E.NNQNPWTFERIVTANMLG
Retrocopy IVEXXXXGGAVNSK<EVQGFLEQVAHKLPFPVKAVSRETLDKMRELQEEREGNNQNPWTFERIVTANMLG

Parental  IRKVLSPYDLTQKGRYWGKFYLPERV
          I.KVLSPYDLTQKGRYWGKFYLPER.
Retrocopy IWKVLSPYDLTQKGRYWGKFYLPERM

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_389 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014289	1 retrocopy	retro_amel_1231,
Canis familiaris	ENSCAFG00000031711	2 retrocopies	retro_cfam_393, retro_cfam_865,
Dipodomys ordii	ENSDORG00000015111	1 retrocopy	retro_dord_389 ,
Felis catus	ENSFCAG00000007540	2 retrocopies	retro_fcat_479, retro_fcat_639,