RetrogeneDB ID: retro_dord_159

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_4074:69546..70009(+)
• Located in intron of: ENSDORG00000008724

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mtx2
• Ensembl ID: ENSDORG00000003848
• Aliases: None
• Description: metaxin 2 [Source:MGI Symbol;Acc:MGI:1859652]

Sequence

>retro_dord_159
AAAGAAGCAGAAATGGAAGCTGACTTGGAACTAGTCAACAGTGTGCAGGTGGCTGTGGAGTTGCAGTGGTGGGCTGAAGT
TCCTGTTGGGGAGGTGAGCAAATTCTAGGCATGGATCTCCTTACTCTTGGCCTCTGAATCATGTTTTGGCCTATCAGAAG
CCATCTCACCAAGGTGAGATGAAAGCAATTGGATGGGGTAAAGCTAGTGGGCCCAGAATAGGCCAAGGTCAAATAGACGA
TGGAGATCAGTTCTACCAAGCTGTTTCTCAAAGACTGGAAACATAACCAGATTTATTCAATAAGCAATCTGCTGAACTTG
ATGTGTCAATATTTGGCCTTTTATATGCCATTGCCACCATTCAGCTGACCAATGGTGAACTTTCTGAGAAGGTGAAAAAC
TATAGCAACCTCCTTGTTTTCTGTAGAACTGAGCAGCACTATTTTGAAGATTGTGATCAAGGC

Alignment

ORF - retro_dord_159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.35 %
• Parental protein coverage: 58.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QKAEMKAYMELVNNMLLTAELYLQWCDEATVEEIT-HSRYGSPYPWPLNHILAYQKQWEVKRKMKAIGWG
          ..AEM.A..ELVN......EL..QW..E..V.E....SR.GSPY.WPLNH.LAYQK.......MKAIGWG
Retrocopy KEAEMEADLELVNSVQVAVEL--QWWAEVPVGEVS>NSRHGSPYSWPLNHVLAYQKPSH-QGEMKAIGWG

Parental  NKTLDQV----LEDVDQCCQALSQRLGTQPYFFNKQPTELDALVFGHLYTILTTRLTNDELCEKVKNYSN
          .............D.DQ..QA.SQRL.T.P..FNKQ..ELD...FG.LY.I.T..LTN.EL.EKVKNYSN
Retrocopy KASGPRIGQGQIDDGDQFYQAVSQRLET*PDLFNKQSAELDVSIFGLLYAIATIQLTNGELSEKVKNYSN

Parental  LLAFCRRIEQHYFEDRGRG
          LL.FC.R.EQHYFED...G
Retrocopy LLVFC-RTEQHYFEDCDQG

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_159 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009655	1 retrocopy	retro_chof_2429,
Cavia porcellus	ENSCPOG00000011099	1 retrocopy	retro_cpor_218,
Dipodomys ordii	ENSDORG00000003848	2 retrocopies	retro_dord_159 , retro_dord_192,
Homo sapiens	ENSG00000128654	1 retrocopy	retro_hsap_3780,
Macaca mulatta	ENSMMUG00000010185	1 retrocopy	retro_mmul_1643,
Nomascus leucogenys	ENSNLEG00000006020	1 retrocopy	retro_nleu_1117,
Pan troglodytes	ENSPTRG00000012674	1 retrocopy	retro_ptro_2561,
Sarcophilus harrisii	ENSSHAG00000016381	1 retrocopy	retro_shar_162,