RetrogeneDB ID: retro_dord_565

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_33234:13916..14295(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tvp23a
• Ensembl ID: ENSDORG00000015782
• Aliases: None
• Description: trans-golgi network vesicle protein 23A [Source:MGI Symbol;Acc:MGI:3665441]

Sequence

>retro_dord_565
ATGGTGACAATTATCTTGTTGTCATGTGACTTTTGGGCTGTGAAGAATGTTACAGATAGACTAGTGGTCAGCCTCCATTG
GCGGAATCATATTGATGAGGATGGAAAAAGCCACTGGGTGTTTGAGTCCAGAGAGGCAACTCCTCAAGATAATAAAACTG
TTTCAGAAGCTGAATCAAGAATCTTTTGGTTGGGACTTACTGCCTTTTCAGTGCTGTGGGTGATATTTGCCTTCAGTGCT
CTCTTCTCCTTCAGAGTCAAGTGGGTTGGCTGTGGTTATTATGGATGTGGTACTACAAGGTGCCAACCTGTATGGTTACA
TATGTGTAAAGTGGCAGCAGAAGAACTTAACTACCATGGCTACCTTGTATCTTGGAAAG

Alignment

ORF - retro_dord_565 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.78 %
• Parental protein coverage: 69.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VTVLLLLAFDFWSVKNVTGRLLVGLRWWNQIDEDGRSHWVFEARKASPHHVAT-TEAEARIFWLGLIICP
          .....LL..DFW.VKNVT.RL.V.L.W.N.IDEDG.SHWVFE.R.A.P....T..EAE.RIFWLGL....
Retrocopy MVTIILLSCDFWAVKNVTDRLVVSLHWRNHIDEDGKSHWVFESREATPQDNKTVSEAESRIFWLGLTAFS

Parental  LIWMVFFFTTLFSLKLKW-LALVVAGISLQAANLYGYILCKMGGDSDLSKVAASFLSQ
          ..W..F.F..LFS...KW.LA.V.....LQ.ANLYGYI.C.......L...A...L..
Retrocopy VLWVIFAFSALFSFRVKW>LAVVIMDVVLQGANLYGYI-CVKWQQKNLTTMATLYLGK

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_565 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015782	2 retrocopies	retro_dord_528, retro_dord_565 ,
Nomascus leucogenys	ENSNLEG00000010137	1 retrocopy	retro_nleu_2447,
Pongo abelii	ENSPPYG00000007094	1 retrocopy	retro_pabe_1344,
Tursiops truncatus	ENSTTRG00000015641	1 retrocopy	retro_ttru_1286,