RetrogeneDB ID: retro_shar_248

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834942.1:44337..45106(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000011925
• Aliases: None
• Description: None

Sequence

>retro_shar_248
ACTTCAACACCATCACTAGCTACAATTCAACAACCAAATTCTGCTGCTACTACTAATTCTAGTTCATCTACAACAGTATC
TGTGACTCAAGCCACTTCCCTTAGCCTCCACCCCTATTCCTAAACCTGAACTCAATACCATCTGCAGGGGCTTGGGAACC
TAAACCCAGAGGTGTTCCTAAGGAAGAGAACCCAGTCAAACCTCCTATTGATATTAGCCCAACATCATCTGTCAAAAGCT
CGGGGGGTCTCTCTTAGGTCAAACTATTTTGAAGATGCAACAAGTGCTCTTGTGATGGGACAATCTTATGAAAATATGGT
GATTGAGATCATGTCAATGGATATGAAAGAGAATAAGCTATCATAGTACTGGGAATTGATTTCATCACCCTGGTAGAATG
GTGGAACATTTTTAATGGGTATTTAGGGAGATAAAGAGTCAAGCTGTGGTGGATCCCACCCAAGCACCTACCAAGCCTGC
CAACACAGGTTAGTTCAGTCTTCAGTAGTGGCAGCAGCTACAGACACAACAGCAACAACTACAACTCCTAATTCTTCAGG
ACATCCACTTAATTTTTTTATGGAACCAGTCTCAGATCCAGCAAATGAGACAAATTTTTCATCAGAAATTTTCTCTTCTG
TCAACCTTGCTACAGCAAATAGGACTAGAAAATCCACAGTTAATTCAGCAATTCAGTCATTCAAGAGCATTTTATTCAAG
TGCTAAATTGAACCAGTTCTTTGAAGGAGGTGGAGGTGGTAGTGGAGGA

Alignment

ORF - retro_shar_248 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.43 %
• Parental protein coverage: 67.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  TSTPSPATTQQSNPATTTTVSSSSAASVAQAPTPSPALA-PTPTPTSVTPTPAAAACEPIPTSTPKEEKP
          TSTPS.AT.QQ.N.A.TT.....S..S.....T....L..P.P........P.A.A.EP.P...PKE...
Retrocopy TSTPSLATIQQPNSAATT----NSSSSTTVSVTQATSLS<PPPLFLNLNSIPSAGAWEPKPRGVPKE---

Parental  AEKPVEAPVGISPTSSDSTLGDSS-RSNLFEDATSALVTGQSYENMVTEIMSM-GYEREQVIAALRAS-F
          .E.PV..P..ISPTSS....G..S.RSN.FEDATSALV.GQSYENMV.EIMSM.GYERE..I..L....F
Retrocopy -ENPVKPPIDISPTSSVKSSGGLS>RSNYFEDATSALVMGQSYENMVIEIMSM<GYERE*AIIVLGID<F

Parental  NNPDRAVEY-LLMGIPGDRESQAVVDPP---QAASTGAAQSSAVAAAAATTTATTTTTTTSGGHPLE-FL
          ..P.R.VE...LMGI.GD.ES......P...QA......QSS.V..AAAT.T..TTTT..S.GHPL..FL
Retrocopy HHPGRMVEH<FLMGI*GDKESSCGGSHPSTYQACQHRLVQSSVV--AAATDTTATTTTPNSSGHPLN>FL

Parental  RNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQH-QEHFIQMLN-EPVQ-ESGGQGGGG
          .NQ.Q.QQMRQI..Q..SLL..LLQQIG.ENPQL.QQ.S.H.QEHFIQ.LN.EPV..E.GG.G.GG
Retrocopy WNQSQIQQMRQIFHQKFSLLSTLLQQIGLENPQLIQQFS-H>QEHFIQVLN>EPVL>EGGGGGSGG

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_248 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 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Dasypus novemcinctus	ENSDNOG00000001174	2 retrocopies	retro_dnov_1982, retro_dnov_989,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Homo sapiens	ENSG00000119318	2 retrocopies	retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla	ENSGGOG00000002511	1 retrocopy	retro_ggor_1829,
Loxodonta africana	ENSLAFG00000007533	1 retrocopy	retro_lafr_1109,
Macaca mulatta	ENSMMUG00000014944	2 retrocopies	retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys	ENSNLEG00000017319	1 retrocopy	retro_nleu_1590,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Otolemur garnettii	ENSOGAG00000014216	1 retrocopy	retro_ogar_3040,
Pongo abelii	ENSPPYG00000019477	2 retrocopies	retro_pabe_2344, retro_pabe_3162,
Pan troglodytes	ENSPTRG00000021229	1 retrocopy	retro_ptro_1760,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248 ,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,