RetrogeneDB ID: retro_shar_437

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL842993.1:10612..11050(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCUN1D4
• Ensembl ID: ENSSHAG00000017879
• Aliases: None
• Description: DCN1, defective in cullin neddylation 1, domain containing 4 [Source:HGNC Symbol;Acc:28998]

Sequence

>retro_shar_437
CATTTGGATGTTGCCACTGTCAATTTTCAGTTTAATTTTCATCTCTCAACAGTGACAAATATTGACAAGATAGACCACAC
ACTTAATAAGTAGAGTTTAATGGAAGACATTGAGCAAAACAATCATCAAATGGGAAGTCTTGAATTTTGCAGTTTATCAG
ACTGCATTAGCAAAGTAATGCCATCAAGAAAAAAGAGAAAATCCACTGCTGGATATGATTTACTTGCAAAGAAAAGTAGA
TACAGTAGTAAGTATAGGAAATATGATTCAGCTAGAATAACGACTGAGGAAGAAACGTTTTCAAGTAAGAGATGCTTGGA
GTGGTTCTGTGACTATGCAGGGACTGATGATGTTCTAGTCCAGGCCCTGAAAGCTTGGAGAAAGAAAGACATTGGAGTAA
AACCTTAAAATGTACTCATGTTTGCATTAACTTGGAAA

Alignment

ORF - retro_shar_437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.59 %
• Parental protein coverage: 50.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HSDISFVIDFQLNSHLSTLANIHKIYHTLNKLNLTEDVGQDDHQTGSLRSCSSSDCVSKVMPPRKKRRPA
          H.D......FQ.N.HLST..NI.KI.HTLNK..L.ED..Q..HQ.GSL..CS.SDC.SKVMP.RKKR...
Retrocopy HLDVA-TVNFQFNFHLSTVTNIDKIDHTLNK*SLMEDIEQNNHQMGSLEFCSLSDCISKVMPSRKKRKST

Parental  AGDDLSAKKSRHDSMYRKYDSTRIKTEEETFSSKRCLEWFYEYAGTDDVVGPEGMEKFCEDIGVEPENVV
          AG.DL.AKKSR..S.YRKYDS.RI.TEEETFSSKRCLEWF..YAGTDDV...........DIGV.P.NV.
Retrocopy AGYDLLAKKSRYSSKYRKYDSARITTEEETFSSKRCLEWFCDYAGTDDVLVQALKAWRKKDIGVKP*NVL

Parental  MLVLAWK
          M..L.WK
Retrocopy MFALTWK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_437 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018601	1 retrocopy	retro_cjac_3959,
Cavia porcellus	ENSCPOG00000008945	2 retrocopies	retro_cpor_1176, retro_cpor_1179,
Sarcophilus harrisii	ENSSHAG00000017879	1 retrocopy	retro_shar_437 ,