RetrogeneDB ID: retro_dord_268

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_6829:688955..689824(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Slc25a4
• Ensembl ID: ENSDORG00000013787
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 4 [Source:MGI Symbol;Acc:MGI:1353495]

Sequence

>retro_dord_268
GTGTCCTTCTGGAAGGAACTGCTGGCCAGCGGTGTGGTAGCAGCCATGTCGAAGACGGCGGTGGCGCCCATCGAGCAGGT
GAAGCTGCTGCTGCAGGTGCAGGCGTCCTACAAGCAAATCAGCCCCGAGGCCCAGTACAAGGACTTGGTGGACTGCCTGG
TACGGATTCCCCATGAGCAGGGTTTCTTCAGTTATTGGAGTGGCAATTTGCGAATGTTATCAGGTATTTTCTAACATAAG
CTCTAAATTTTGCTTTCAAAGACAAATACAAACAGCTTTTCATGTCGGGGGATAATAAAGAAAAATATTTCTGGAGGTGG
TTTTTGGCAAATCTGGCTTCTGGTGGAGCTGCTGGAGCAACATCCTTATGTGTAGTATTTCCACTGGATTTTGTCCAAAC
CCATTTAGGTGTTGATATTGGAAAAGGTCCTCAAGAGAGACAGTTCAAGGGTTTTGGTGACTGTATTATGAAAATAGCAA
AATCAGAAGGAATTATTGGCTTATACCAAGGATTTAGTGTTTCAGTTCAGGGCATTATTGTGTACTGAGCCTCTTACTTT
GGAGCTTATGACACAGTTAAGTGCTTGTTACACAAACCAAAGGAAACCCCATTTCTTGTTTCCTTTATCATTGCTCAAAT
TGTGACTACATGTTCTAGAATACTCTCTTATCCCTTTGACACAGTTAGAAGACATGATGATGCAGAGTGGTGAGTCTCAG
CGGCAAAATAAAGGAACATTAGACTGCTTTATGAAAATATACCAACATGAGAGAATTGGTGCATTTTTTCGTGGTGCCTT
CTCCAACATCCTTCGAGGTACAGGGGTGTTTTGGTGTTAGTGTTATATGACAAATTTAAAGAATTCCTT

Alignment

ORF - retro_dord_268 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.84 %
• Parental protein coverage: 98.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSFLKDFLAGGIAAAVSKTAVAPIERVKLLLQVQHASKQISAEKQYKGIMDCVVRIPKEQGFLSFWRGNL
          .SF.K..LA.G..AA.SKTAVAPIE.VKLLLQVQ...KQIS.E.QYK...DC.VRIP.EQGF.S.W.GNL
Retrocopy VSFWKELLASGVVAAMSKTAVAPIEQVKLLLQVQASYKQISPEAQYKDLVDCLVRIPHEQGFFSYWSGNL

Parental  -ANVIRYFPTQALNFAFKDKYKQIFLGGVDRHKQFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAAD
          .ANVIRYF.T.ALNFAFKDKYKQ.F..G....K.FWR.F..NLASGGAAGATSLC.V.PLDF..T.L..D
Retrocopy <ANVIRYFLT*ALNFAFKDKYKQLFMSGDNKEKYFWRWFLANLASGGAAGATSLCVVFPLDFVQTHLGVD

Parental  VGKGASQREFNGLGDCLTKIFKSDGLKGLYQGFSVSVQGIIIYRAAYFGVYDTAKGMLLDPKNVHIIVSW
          .GKG...R.F.G.GDC..KI.KS.G..GLYQGFSVSVQGII.Y.A.YFG.YDT.K..L..PK.....VS.
Retrocopy IGKGPQERQFKGFGDCIMKIAKSEGIIGLYQGFSVSVQGIIVY*ASYFGAYDTVKCLLHKPKETPFLVSF

Parental  MIAQSVTAVAGLVSYPFDTVRRR-MMMQSGRKGADIMYTGTLDCWRKIAKDEGGKAFFKGAWSNVLRGMG
          .IAQ.VT......SYPFDTV.RR.MMMQSG.........GTLDC..KI...E...AFF.GA.SN.LRG.G
Retrocopy IIAQIVTTCSRILSYPFDTV-RR>MMMQSGE--SQRQNKGTLDCFMKIYQHERIGAFFRGAFSNILRGTG

Parental  -GAFVLVLYDEIKKYV
          .G..VLVLYD..K...
Retrocopy <GVLVLVLYDKFKEFL

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_268 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 13 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013208	1 retrocopy	retro_btau_1592,
Choloepus hoffmanni	ENSCHOG00000010542	3 retrocopies	retro_chof_1117, retro_chof_1777, retro_chof_807,
Dasypus novemcinctus	ENSDNOG00000007258	3 retrocopies	retro_dnov_1531, retro_dnov_1800, retro_dnov_390,
Dipodomys ordii	ENSDORG00000013787	1 retrocopy	retro_dord_268 ,
Erinaceus europaeus	ENSEEUG00000001021	2 retrocopies	retro_eeur_274, retro_eeur_36,
Macropus eugenii	ENSMEUG00000008508	4 retrocopies	retro_meug_222, retro_meug_549, retro_meug_6, retro_meug_921,
Microcebus murinus	ENSMICG00000010865	1 retrocopy	retro_mmur_1356,
Oryctolagus cuniculus	ENSOCUG00000002594	1 retrocopy	retro_ocun_102,
Ochotona princeps	ENSOPRG00000005957	6 retrocopies	retro_opri_1154, retro_opri_146, retro_opri_377, retro_opri_517, retro_opri_543, retro_opri_685,
Pan troglodytes	ENSPTRG00000016646	9 retrocopies	retro_ptro_146, retro_ptro_1588, retro_ptro_2143, retro_ptro_2364, retro_ptro_2388, retro_ptro_2517, retro_ptro_2525, retro_ptro_2819, retro_ptro_2882,
Pteropus vampyrus	ENSPVAG00000015279	1 retrocopy	retro_pvam_892,
Sarcophilus harrisii	ENSSHAG00000000932	1 retrocopy	retro_shar_160,
Tarsius syrichta	ENSTSYG00000004233	1 retrocopy	retro_tsyr_27,