RetrogeneDB ID: retro_shar_796

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL864869.1:1334952..1335250(-)
• Located in intron of: ENSSHAG00000013362

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNRD1
• Ensembl ID: ENSSHAG00000001554
• Aliases: None
• Description: zinc ribbon domain containing 1 [Source:HGNC Symbol;Acc:13182]

Sequence

>retro_shar_796
TTTGCCATGGACCTTCCTCTTCTCTCAGCCTCTTAGAACTCCCTATCAATTTTATGTTTAAACCCTGAATCTGGTTCCAC
TTTTTTTCTTGTTGGGATTTTGGATATAGATATTTGTCCCAGATATGATTTCTCCATAGACATGTGGGATTTCAAGGGGA
AAGTGGAGAAGACATCAGTCGTGTTCCACAAATTGAGAACAACTTCCTTGTTGGTATCTAAATAGCCTGAAATCTAGGGA
GCAGTGACCGACAAATGCTGGTTCCACCTGTGGCTGTGAGGGTGTGGCATATTATACC

Alignment

ORF - retro_shar_796 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.98 %
• Parental protein coverage: 75.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FAMDPSAASSSFLSDSDFCT--ECGSILPLPGALDTVTCPRCGFSIDVREFEGKVVETSIVFHKLGTTAL
          FAMD....S.S..S.S..C...E.GS...L.G.LD...CPR..FSID...F.GKV..TS.VFHKL.TT.L
Retrocopy FAMDLPLLSAS*NSLSILCLNPESGSTFFLVGILDIDICPRYDFSIDMWDFKGKVEKTSVVFHKLRTTSL

Parental  IVSEEEGPELQGPVIDR-RCSNCGHEGMAYHT
          .VS....PE..G.V.D....S.CG.EG.AY.T
Retrocopy LVS--K*PEI*GAVTDK>AGSTCGCEGVAYYT

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_796 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 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007328	2 retrocopies	retro_chof_1997, retro_chof_2061,
Dasypus novemcinctus	ENSDNOG00000015720	9 retrocopies	retro_dnov_1020, retro_dnov_1103, retro_dnov_1472, retro_dnov_1726, retro_dnov_1798, retro_dnov_1881, retro_dnov_2400, retro_dnov_2420, retro_dnov_933,
Myotis lucifugus	ENSMLUG00000007272	1 retrocopy	retro_mluc_126,
Monodelphis domestica	ENSMODG00000016023	1 retrocopy	retro_mdom_1799,
Mustela putorius furo	ENSMPUG00000007474	1 retrocopy	retro_mputfur_968,
Rattus norvegicus	ENSRNOG00000000779	1 retrocopy	retro_rnor_978,
Sorex araneus	ENSSARG00000009716	2 retrocopies	retro_sara_431, retro_sara_745,
Sarcophilus harrisii	ENSSHAG00000001554	1 retrocopy	retro_shar_796 ,