RetrogeneDB ID: retro_shar_660

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856949.1:619563..620150(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPPL3
• Ensembl ID: ENSSHAG00000015326
• Aliases: None
• Description: signal peptide peptidase like 3 [Source:HGNC Symbol;Acc:30424]

Sequence

>retro_shar_660
CTGCCAAGCCACAAAATCTTCTGTTTTCTCCTTTTAGACCCTCTGATCTGAGATGTCTTCTGGGTTTTTTTTTTTTCTTC
CACCTACATTTTTATAGTAGCATCATGGTCAAAATTGTCACCTAGCCAGCAGCTTACCCCTTTGACATTCTATGCAAGAA
GCTTCATCTGGGACCAAATGTGGACTGACATTTCTTGATTGTCTTTTCCTGAAAAAAATAGTTTTTCTGAGTTCCATAGG
CAGTCATTCTTTATATGGGAATTGGTGATATGGTGATGCCAGGACTCTTCCTGTCTTTTGTGCTATGCTATATTAACCAT
AAGAAACAGGAAAGAAGTGACTCCTGTGGGAATCTGGGACTGGGGCATATCTTGGGCCAAATGAAGAAGGTTTCCTATTT
TCCCTACACTCTCATTGGATCCTTTGTAAATCTTATCAATACAACAGTAGTAGTGTCTCTGATCCATTGAACTGCTCAGT
CTGTACTCCTCTGTATGGTACCATTCACTTTGTTGCCACTTCTCACAATGACTTACTTAAGAGGAGATCTGTGCCACATG
TGGTCTCACTCTCAGGCTCATGGTTCC

Alignment

ORF - retro_shar_660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.22 %
• Parental protein coverage: 51.04 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LPSLKVSCLLLSGLLIYDVFWVFF--SAYIF-NSNVMVKVATQPAD-NPLDVLSRKLHLGPNVGRDVPRL
          LPS.K..C.LL...LI.DVFW.....S.YIF..S..MVK..T.PA...PL....R..........D...L
Retrocopy LPSHKIFCFLLLDPLI*DVFWXXXXXSTYIF<YSSIMVKIVT*PAA>TPLTFYARSF-IWDQMWTDIS*L

Parental  SLPGKLVFPSSTGSHFSM-LGIGDIVMPGLLLCFVLRYDNYKKQASSDSCGAPGPGNISGRMQKVSYFHC
          S.P.K..F.......F....GIGD.VMPGL.L.FVL.Y.N.KKQ..SDSCG..G.G.I.G.M.KVSYF..
Retrocopy SFPEKNSFSEFHRQSFFI<MGIGDMVMPGLFLSFVLCYINHKKQERSDSCGNLGLGHILGQMKKVSYFPY

Parental  TLIGYFVGLL-TATVASRIHRAAQPALLYLVPFTLLPLLTMAYLKGDLRRMWSEPFHSKASSS
          TLIG.FV.L..T..V.S.IH..AQ..LL..VPFTLLPLLTM.YL.GDL..MWS...HS.A..S
Retrocopy TLIGSFVNLINTTVVVSLIH*TAQSVLLCMVPFTLLPLLTMTYLRGDLCHMWS---HSQAHGS

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_660 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016589	1 retrocopy	retro_dnov_175,
Homo sapiens	ENSG00000157837	1 retrocopy	retro_hsap_1898,
Gorilla gorilla	ENSGGOG00000016245	1 retrocopy	retro_ggor_1392,
Myotis lucifugus	ENSMLUG00000012754	1 retrocopy	retro_mluc_672,
Macaca mulatta	ENSMMUG00000020650	1 retrocopy	retro_mmul_1359,
Pongo abelii	ENSPPYG00000005041	2 retrocopies	retro_pabe_1578, retro_pabe_1579,
Pan troglodytes	ENSPTRG00000005548	1 retrocopy	retro_ptro_1275,
Rattus norvegicus	ENSRNOG00000001178	1 retrocopy	retro_rnor_2157,
Sarcophilus harrisii	ENSSHAG00000015326	1 retrocopy	retro_shar_660 ,