RetrogeneDB ID: retro_shar_665

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856967.1:1118231..1120346(-)
• Located in intron of: ENSSHAG00000012329

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000006165
• Aliases: None
• Description: None

Sequence

>retro_shar_665
AAACTGAAGAAGCTACTAAAACATCTGAAGAAACCCTCAGACTTACCTATCACTGTGGACATTCTGGCGGAAACAGGTGT
TGGGAAAACAGTGAATGGCTGGTGGAAACATGAGCAAGTAGGAGGCTTTGCCAAAGATTTAGTGGCCCGATGGAAGAAGT
TAGTCCCTGTTGCTTAGGAGGTTGAAAGGAATATTGAGCCTGAGGAGCAAATGCTTGAGAGAAGTAGCTCTAGAAAACAT
CCCCGAGATGTTTTTCCCAAGGAGGAGGAAATGGAGGAGGAATATCAGGAAAGCTGGAAGGACTCTTGTAGCCAGTCATA
CTGACTCCCAGGAGAAAAAGCATGGAAAACTTTCAGAGTTTGGTAGAGTGCCCAAGGCCTCACACAGTAGTAAGACAAGA
GAAGAGAGAAGGCCATGGAAGAAAACCTCCTCATTGTACACATACGATCAGGAACCATTCAACAGAAGTCATGTTCACTC
ACCTCAGCCTTCCACAAGCCCTTAGCAATTATCCATGATCAACTCCCTGAAGAGGAGGAGGAGCAGCTGATACCACATCA
GAAGGCTGGCAAAAGCCATAGATAGTCATGCCTTTCAGGACCAAGGCTAAAATAGCCAAGAGAGATACGTAGGTGAACCC
CGGGACAAAGGCCTTGTGAGTCAGAGCAAAAAGCACAAGACTTCCCAGAAAGAAAAGCATCGCTTGGATAAAAGAGAGGA
AAAGAACTTTAGTTTGGGTTGAGGCAAAGTGTCTAAGGCTGTTTCTCGAGAAGAGGGCCAAAGTATCCCTCAGGAACCAG
TACTAAGGAGAAGCAGACATTGTCTAGTGCTGCCAAGAAAGAGAGGGACAAAGAAAGCGTCAGTAGCAAGAAGTTTTTAC
CTCCCTTGGAGGTGGCTTCTGTCAACCATATGAAAAAAACAAAGCACAAGGATGCACAGAAATCCAAATTGGAAAAGACC
AAGCTTAGTGTGGACAGCTTTGATGTAGGAAAGTGGGAGGGAGAATTTTCTCCCAAGCCAAAAGAGAAAGGGGTGTCTAA
TAGCTTAAAGGAAAATTCAAAGCCCTTAACTCAGACAGAAAACCATCGAGTCACTTTTCAGGGGCTTGAGAGACAGATAT
GGATGATGTCTATGAATAGCCCACCACGTCTTTTGAATCATACCCCAGCTACGACCAGCCCCAGAGGGGAAAAAAAAGGT
TGTTAAAACTACAAGTGGGATTCGTGCAGAGAAAAGTCACAATAAGCAGAATGGTTTCAAAGCTGATCATAAAAACTCTA
ATAATATCATTCAGAAACTCCCTAAGATGAGTGAGAGCAAGGCAGAAAAGCAACTTTCTGGAGCCAGCTCTGCCAAACTA
AAAACAGTCTCCATTGATGTGATGCCAACATTACCGGACATCCCCTTGCCTACCATTTAGGCCATTTATCACCCACTTCC
TTCTCTTAAACTGATTCCCTCCTTTTAGCCAAAGAGGAAAGAACCCTCACCCCATGAAGAAGAGGAAGCTGGATTTACTG
GATGTAGGATGAATTCAAAAATGCAAGTCTATTCTGATTCCAAGTGTGCCTACCTATCGAAGATGATGTCCATGCACCAG
CAGTGCACTGGAGTCCTCAATAATAGCATAGACTCAATTTATGAAGTTGGGGGTATTCCCTATTCTGTACTTGAACCAGT
TTTGGAAAGATGTACTCCTGAGCAACCCTATGGAATTGAGGAGTGCAGCCATGTGTTACACGAAGAGACTGATCAGCTGA
GGAAAATTCACTGCCATAGGGACTTTAAGAGAGAGAGACCAGAAGAATTTGGGTCTTGGAGGGAGGTGAGTCTTCAGCTC
CGGGATGCTCGGGAGCAGGGACTGCTCCTCTTAGCTGAGAACATTCGATCAGCTCATGCCAACAAACCCAAAGGCCGACA
AGCAAAGATGGCCTTTGTCAACTCTGTGGCCAAGTCGCCTCTGATGTCAGGAGACAGCAGGAGAAATGTGGGACTGGAGG
AGCGGCTGTTCCCAAAAAGATCAAGGTCAAACCCACCCCCTACACCTCCAGCAATAGCTACATCTGCAGCAGGGGGTGCA
GCAGCGCCAAGGAAGGGCAGCCCTACAACGGCCCC

Alignment

ORF - retro_shar_665 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.14 %
• Parental protein coverage: 90.85 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  KKKKLLKHLKRLSDLPITVDILAETGVGKTVNGLRKHEQVGGFAKDLVARWKKLVPVA----QNIEPEEQ
          K.KKLLKHLK..SDLPITVDILAETGVGKTVNG..KHEQVGGFAKDLVARWKKLVPVA.....NIEPEEQ
Retrocopy KLKKLLKHLKKPSDLPITVDILAETGVGKTVNGWWKHEQVGGFAKDLVARWKKLVPVA*EVERNIEPEEQ

Parental  DLERSSSRKRPRDV-FPKEEEMEEEYQESWKASCSQPHSPDYREKKHRKLSEFDRMPKASHSGETREERK
          .LERSSSRK.PRDV.FP....................H..D..EKKH.KLSEF.R.PKASHS..TREER.
Retrocopy MLERSSSRKHPRDV>FPRRRKWRRNIRKAGRTLVAS-HT-DSQEKKHGKLSEFGRVPKASHSSKTREERR

Parental  RWNKTSPLYTSDQELSDSSHVHSPQPSTSP-QQLSMDYDQLPEEEEEEQPVPH-RKAGKS-HSHAFQDRG
          .W.KTS.LYT.DQE....S..H...P..S....L....DQLPEEEEE.Q..PH.R...K...SHAFQD.G
Retrocopy PWKKTSSLYTYDQEPFNRS--HVHSPQPST<KPLAIIHDQLPEEEEE-QLIPH>RRLAKAIDSHAFQDQG

Parental  LNSQERRLGEPQDRGSVSRSKEHKTSQKEKHRLDTREEKTFSLGRDKVSKAVSREEGR-RSPSGASTKEK
          .NSQER..GEP.D.G.VS.SK.HKTSQKEKHRLD.REEK.FSLG..KVSKAVSREEG....PSG.STKEK
Retrocopy *NSQERYVGEPRDKGLVSQSKKHKTSQKEKHRLDKREEKNFSLG*GKVSKAVSREEGQ<KYPSGTSTKEK

Parental  QTLSSAAKKERDKESGGSKKKLLPPLEVASVNHMKKTKHKDAQKSKLEKTKLSGDSFDVGKWEGEFSPKP
          QTLSSAAKKERDKES..SKK..LPPLEVASVNHMKKTKHKDAQKSKLEKTKLS.DSFDVGKWEGEFSPKP
Retrocopy QTLSSAAKKERDKESVSSKK-FLPPLEVASVNHMKKTKHKDAQKSKLEKTKLSVDSFDVGKWEGEFSPKP

Parental  KEKGGSNSLKTREGKPKASNSDRKSSSHFSG-AGETDVDDDYEQPTMSFESYLSYDQPQRK-KKKVVKTT
          KEKG.SNSLK....KP............F.G.A.ETD.DD.YE.PT.SFESY.SYDQPQR.....VVKTT
Retrocopy KEKGVSNSLK-ENSKPLTQTENHRVT--FQG<A*ETDMDDVYE*PTTSFESYPSYDQPQRX<XXXVVKTT

Parental  TGVRAEKSHSKQNGSKADHKNSNNAIQKLPKMNESKAEKQHSGTSSAKLKKVSTDVTPTLPDIPLPTIQA
          .G.RAEKSH.KQNG.KADHKNSNN.IQKLPKM.ESKAEKQ.SG.SSAKLK.VS.DV.PTLPDIPLPTI.A
Retrocopy SGIRAEKSHNKQNGFKADHKNSNNIIQKLPKMSESKAEKQLSGASSAKLKTVSIDVMPTLPDIPLPTI*A

Parental  NYRPLPSLELIPSFQPKRKAVSSPHEEEEAGFTGRRMNSKMQVYSGSKCAYLPKMMSLHQQCIRVLNNNI
          .Y.PLPSL.LIPSF.PKRK...SPHEEEEAGFTG.RMNSKMQVYS.SKCAYL.KMMS.HQQC..VLNN.I
Retrocopy IYHPLPSLKLIPSF*PKRKE-PSPHEEEEAGFTGCRMNSKMQVYSDSKCAYLSKMMSMHQQCTGVLNNSI

Parental  DSIYEVGGVPYSVLEPVLERCTPEQLYRIEECNHVLTEETDQLWKIHCHRDFKRERPEEFESWREMYLRL
          DSIYEVGG.PYSVLEPVLERCTPEQ.Y.IEEC.HVL.EETDQL.KIHCHRDFKRERPEEF.SWRE..L.L
Retrocopy DSIYEVGGIPYSVLEPVLERCTPEQPYGIEECSHVLHEETDQLRKIHCHRDFKRERPEEFGSWREVSLQL

Parental  QDAREQRLLLLTENIRSAHANKPKGRQAKMAFVNSVAKPP-RDVRRRQEKFGTGGAAVPEKIKIKPAPYT
          .DAREQ.LLLL.ENIRSAHANKPKGRQAKMAFVNSVAK.P..DVRR.QEK.GTGGAAVP.KIK.KP.PYT
Retrocopy RDAREQGLLLLAENIRSAHANKPKGRQAKMAFVNSVAKSP<SDVRRQQEKCGTGGAAVPKKIKVKPTPYT

Parental  SSSGYTCSSSSSSYSNSAEEGQPYDGP
          SS..Y.CS...SS....A.EGQPY.GP
Retrocopy SSNSYICSRGCSS----AKEGQPYNGP

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_665 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011241	1 retrocopy	retro_dnov_1854,
Loxodonta africana	ENSLAFG00000017306	1 retrocopy	retro_lafr_424,
Myotis lucifugus	ENSMLUG00000005258	1 retrocopy	retro_mluc_498,
Monodelphis domestica	ENSMODG00000012842	1 retrocopy	retro_mdom_1961,
Sarcophilus harrisii	ENSSHAG00000006165	1 retrocopy	retro_shar_665 ,