RetrogeneDB ID: retro_shar_235

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834725.1:414017..414270(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC6B
• Ensembl ID: ENSSHAG00000001400
• Aliases: None
• Description: trafficking protein particle complex 6B [Source:HGNC Symbol;Acc:23066]

Sequence

>retro_shar_235
ACAACATTTTTCAAGAAACAAATTGCTTATCTAAGGACAATTTATTAGGGCAGCTATGTGCTTCAAGACAATAAATTTTG
ACTTTTGATTTAGATGTCTTTAGGAAAACAGCATTTGATTTACACGACTAAGCATTTAGCACTTCCAAGTCCCTTATTCA
GAGATAATATAAAATTTGGGCTTAAAAAGTATTTGGACTGCTAAAGTGTCAGCAAGACTAACATGTAAATTTCAAGTGAT
AATACAGAAGATG

Alignment

ORF - retro_shar_235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.98 %
• Parental protein coverage: 62.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TTIFKKQIDNLRTNHQGIYVLQDNKFRLLTQMSAGKQYLDHAPKYLAFTCGLIRGGLSNLGI-KSIVTAE
          TT.FKKQI..LRT...G.YVLQDNKF.LL..MS.GKQ.L....K.LA....L.R......G..KSI.TA.
Retrocopy TTFFKKQIAYLRTIY*GSYVLQDNKF*LLI*MSLGKQHLIYTTKHLALPSPLFRDNI-KFGL>KSIWTAK

Parental  VSAMPACKFQVMIQKI
          VSA...CKFQV.IQK.
Retrocopy VSARLTCKFQVIIQKM

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_235 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013828	1 retrocopy	retro_etel_1104,
Myotis lucifugus	ENSMLUG00000002627	2 retrocopies	retro_mluc_1179, retro_mluc_663,
Mus musculus	ENSMUSG00000020993	2 retrocopies	retro_mmus_1734, retro_mmus_2069,
Oryctolagus cuniculus	ENSOCUG00000002171	1 retrocopy	retro_ocun_813,
Sarcophilus harrisii	ENSSHAG00000001400	1 retrocopy	retro_shar_235 ,
Ictidomys tridecemlineatus	ENSSTOG00000002897	2 retrocopies	retro_itri_476, retro_itri_795,
Tupaia belangeri	ENSTBEG00000003331	1 retrocopy	retro_tbel_4529,