RetrogeneDB ID: retro_shar_304

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841280.1:913926..914900(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000005522
• Aliases: None
• Description: None

Sequence

>retro_shar_304
TATATGGGGAAAGGTATCTCAAAAGTAGCTACGCACATCAATAAATAAATATATTCCCCTGACCATGCTTAGCAAGAAAC
TGAATATTGCAGAGCAGGAGATAATCAATAAGTTGCTGATAGAGATGGACAGCTCCAATAATAAATCTAAATTTATTTCA
AATGCTATATTGGAAGTGTCTCTGGCTATTTGTAAGATCAGAGCTGCTGAGAAAATGGTTTTCCTCTATTGTCATATTGC
TCACCTTTCAGGCAATGACGAAATTATCCTGCCAATTCCAGTCTTCAATGTGATCAATAGTGGCTTTCTTGCTGGTAAAA
AGCTGTTCATGCAAGAGTTCATGATCCTTCCCATTGGAGTAGCAACTTTCAAGGAGGCTCTGAGCACTGGAGCTGAGATT
TACTACAACCTGAAGAATGTGATTAAACAGAAATATGGACAGAACGCTAATGTACAGGATAAGAGTGGCTTTCCTCCTAA
CATTCTAGAGGATAAAGAAGCTCTGGCACTGCTAAAGAATGCTAAAGGCAAAGCTGGCTATATTGATATGGTTGTAATTG
TCATGGATGTTGTTGCCTCAGAATTCTTCTGATCTGGGAAATATGAGTTGGACATCAATTCTGCTGATGATAGTAGGAGA
TAAATCTCTCATTTTGAGTGTGGGGACCTCTACAAGATGTTCATCAAGGACTATTCAGTGGTGTCTATTAAAGATCTTTT
TGATTAGGATGATTTGGGAACTTTGAAAAATTTCACTGCTACTGCAGGTATCTAGGGTAGGAAATCATCTTATCATGATG
AATCTTAAGCACATTGAAAAGATTATGAATGAGAAAGCCTGCAACTTCCTCCTACTCAAAGTAAACCAGATTGACTCCAT
GACTGGATTTCTTTAGGAGTAGGAGCTGGCTCAGTCTAGTGGGTGGAGAGTAATGGTTTCTCCTTTTTTCAGGGAGACTG
AAGATACCTTCATT

Alignment

ORF - retro_shar_304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.55 %
• Parental protein coverage: 74.88 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YMGKGVSKAVEHINKTI-AP-SLISKKLNVVEQEKIDKLMIEMDGSENKSKFGANAILGVSLAVCKAGAA
          YMGKG.SK...HINK.I..P....SKKLN..EQE.I.KL.IEMD.S.NKSKF..NAIL.VSLA.CK..AA
Retrocopy YMGKGISKVATHINK*IYSP>TMLSKKLNIAEQEIINKLLIEMDSSNNKSKFISNAILEVSLAICKIRAA

Parental  EKGVSLYRHIADLAGNSEVILPVPAFNVINGGSHAGNKLAMQEFMILPVGATTFKEAMRIGAEVYHNLKN
          EK.V.LY.HIA.L.GN.E.ILP.P.FNVIN.G..AG.KL.MQEFMILP.G..TFKEA...GAE.Y.NLKN
Retrocopy EKMVFLYCHIAHLSGNDEIILPIPVFNVINSGFLAGKKLFMQEFMILPIGVATFKEALSTGAEIYYNLKN

Parental  VIKQKYGQDATNVGDEGGFAPNILENKEALELLKEAIGKAGYTDKVVIGMDVAASEFFCSGKYDLDFKSP
          VIKQKYGQ.A.NV.D..GF.PNILE.KEAL.LLK.A.GKAGY.D.VVI.MDV.ASEFF.SGKY.LD..S.
Retrocopy VIKQKYGQNA-NVQDKSGFPPNILEDKEALALLKNAKGKAGYIDMVVIVMDVVASEFF*SGKYELDINSA

Parental  DDPSRYISPSELGDLYKTFIKDYPVVSIEDPFDQDD-WEAWKDFTATAGIQVVGDGLTVTNPKRIEKAVN
          DD..R.IS..E.GDLYK.FIKDY.VVSI.D.FD.DD.WE..K..........VG..L...N.K.IEK..N
Retrocopy DDSRR*ISHFECGDLYKMFIKDYSVVSIKDLFD*DD>WEL*K-ISLLLQVSRVGNHLIMMNLKHIEKIMN

Parental  EKACNCLLLKVNQIGSVTESLQACKLAQSNGWGVMVSHRSGETEDTFI
          EKACN.LLLKVNQI.S.T..L....LAQS.GW.VMVS....ETEDTFI
Retrocopy EKACNFLLLKVNQIDSMTGFL*E*ELAQSSGWRVMVSPFFRETEDTFI

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_304 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 17 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003483	2 retrocopies	retro_chof_1289, retro_chof_1811,
Callithrix jacchus	ENSCJAG00000000359	4 retrocopies	retro_cjac_1963, retro_cjac_2238, retro_cjac_3891, retro_cjac_438,
Erinaceus europaeus	ENSEEUG00000008602	2 retrocopies	retro_eeur_23, retro_eeur_243,
Homo sapiens	ENSG00000074800	1 retrocopy	retro_hsap_325,
Macropus eugenii	ENSMEUG00000005942	11 retrocopies	retro_meug_1445, retro_meug_1521, retro_meug_353, retro_meug_472, retro_meug_494, retro_meug_652, retro_meug_664, retro_meug_765, retro_meug_794, retro_meug_874, retro_meug_888,
Macropus eugenii	ENSMEUG00000007840	1 retrocopy	retro_meug_96,
Monodelphis domestica	ENSMODG00000009521	1 retrocopy	retro_mdom_1794,
Mustela putorius furo	ENSMPUG00000006382	2 retrocopies	retro_mputfur_1162, retro_mputfur_547,
Mus musculus	ENSMUSG00000063524	1 retrocopy	retro_mmus_109,
Oryctolagus cuniculus	ENSOCUG00000010086	1 retrocopy	retro_ocun_933,
Otolemur garnettii	ENSOGAG00000004001	1 retrocopy	retro_ogar_1059,
Ochotona princeps	ENSOPRG00000009492	1 retrocopy	retro_opri_969,
Pan troglodytes	ENSPTRG00000000109	1 retrocopy	retro_ptro_261,
Pteropus vampyrus	ENSPVAG00000005030	1 retrocopy	retro_pvam_317,
Rattus norvegicus	ENSRNOG00000017895	1 retrocopy	retro_rnor_112,
Sarcophilus harrisii	ENSSHAG00000005522	1 retrocopy	retro_shar_304 ,
Tarsius syrichta	ENSTSYG00000002509	1 retrocopy	retro_tsyr_2011,