RetrogeneDB ID: retro_dord_362

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_13855:1226..1635(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000000637
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pfdn2
• Ensembl ID: ENSDORG00000004588
• Aliases: None
• Description: prefoldin 2 [Source:MGI Symbol;Acc:MGI:1276111]

Sequence

>retro_dord_362
GCGGGAAGGGGCCCGTGCGGACAGGTAATTGCTGGCTTCAATCGCTTCGGCAAGAGCAACGGGGCCTGGCTTCCAAAGCA
GCTGAGCTAGAGATGGAGCTGAATGAGCACAGCTAGTGATTGATACACTGAAAGAAGTCGATGAAACTCGAAAGTGCTTC
CGTACGGTTGGAGGTGTGCTGGTAGAGCGGACTGTCAAAGAGGTGCTGCCTGCCTTGGAGAATAACAAGGAACAGATACA
GAAGATCATTGAGACATTGTCACAGCAACTTCAGGCAAAGGGAAAAGAACTAAATGAATTCCGGGAAAAGCACAACATTC
GTCTTATGGGGGAAGATGAGAAGCCAGCAGCCAAGGAAAACTCAGAAGGGTCTGGGGCTAAGGCCAGTTCTGCTGGAGTA
TTGGTCTCC

Alignment

ORF - retro_dord_362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.62 %
• Parental protein coverage: 90.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGKGAVSAEQVIAGFNR-LRQEQRGLASKAAELEMELNEHS-LVIDTLKEVDETRKCFRMVGGVLVERTV
          AG.G.....QVIAGFNR.LRQEQRGLASKAAELEMELNEHS.LVIDTLKEVDETRKCFR.VGGVLVERTV
Retrocopy AGRGPCG--QVIAGFNR<LRQEQRGLASKAAELEMELNEHS<LVIDTLKEVDETRKCFRTVGGVLVERTV

Parental  KEVLPALENNKEQIQKIIETLSQQLQAKGKELNEFREKHNIRLMGEDEKPAAKENSEGSGAKASSAGVLV
          KEVLPALENNKEQIQKIIETLSQQLQAKGKELNEFREKHNIRLMGEDEKPAAKENSEGSGAKASSAGVLV
Retrocopy KEVLPALENNKEQIQKIIETLSQQLQAKGKELNEFREKHNIRLMGEDEKPAAKENSEGSGAKASSAGVLV

Parental  S
          S
Retrocopy S

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_362 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000004588	1 retrocopy	retro_dord_362 ,
Myotis lucifugus	ENSMLUG00000004526	1 retrocopy	retro_mluc_1293,
Mus musculus	ENSMUSG00000006412	1 retrocopy	retro_mmus_307,
Tupaia belangeri	ENSTBEG00000015982	1 retrocopy	retro_tbel_2807,
Tursiops truncatus	ENSTTRG00000009181	1 retrocopy	retro_ttru_1756,