RetrogeneDB ID: retro_shar_33

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867616.1:441747..443040(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000008608
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000009886
• Aliases: None
• Description: None

Sequence

>retro_shar_33
ATGTCAGAGTTTTGGTTAGTTTCTATCCCGGGAAACAGGGAGGATTTGGAGATCCTGGAGCAGGTGCTCACTTTCACCTC
CAAGTCCAACCTGTCCCTTAATACCGACTTCGAGATTCCCGATTTCAAGGTAGGGACTTTAGATTCTCTCATTAGCCTTT
CAGACGAACTAGGGAGACTCGATCCCTTTGCCGAAAGCCTAATGAAGAAAATGACTCAGTGTGTTATAGAAGTGACGGAA
GCCAAGAAAGGTGAAGTACAGGAGTACCTCTTGGCCCATGGAGTCACCTTAGCTTCTTTTGTGACTCACTTTGAATGGGA
TTTGATCAAATATCCGGTTAAGCAGCCGTTGGGGGAGGTAGTGGAAGCGTTAAGGAAGCAGCTGACCCAAGTGGAGACAG
ATCTGAAAACCAGAATCTCGGCCTACAAGAAACTGAAAAGAAACCTAGAGACTATGGAAAAAAAACTGTTGGGGGGCCTC
CTCACTCGGTCACTGTCAGATATCGTGAGCAAAGAGGATTTCGTATTGGATTCCAAATACCTCGTCACCCTTCTGGTCAT
CGTTCCCAAGACGAGTTATCCTCTGTGGCAGAAAACGTACGAATCCCTCTCGGACATGGTGGTCCCTCGATCGACCAAGC
TGATCGCCGAAGACAACGAGAGCGGCCTCTTTACCGTCACCATGTTCCAGAAAGTGATCGAGGATTTCAAAATCAAGGCC
ACAGCCAACAAGTTCAAGGTTCGCGACTTTTTTTATGACGAAAAAGAAATCGAAAGCGAAAGGGAAGAAATCACCAAGTT
GCTGGCTGCGAAGAAACAACAAGAGAGTTTCCGAAAGATTCAGAAAAAGCAATCCTTTTCCCTCCTAGATCTTTTTGTGA
AGGCCTTCACTTCGGTTATTCCCCGGAGGTATCAGAAACAACCGAAAGCAAAAGCTCAAGAGAACGAGAGGGAGGCTGAG
GGTGAAGGCTACTGGGAAAATCCTTATTTGCAATGGCTCAAGGCGTGCTTTGGTGAAGTATTTATCATCTTGCTTCACAT
AAAGACCTTAAGAGTGTTTTCTGAATCCGTATTAAGATATGGCCTACCGGTGAATTTTAAGGCAGTACTGCTACAGCCCC
AGAAGAAATCTTCCAAACGGCTCCGGGAAGCTCTCAACTCGGCTTTCAAGCATCTGGACGAAGTGGCGGCCAGTATCATG
GATATCTCTCTAGATATCCCTGGGTTACAACTCGGCAACCAGGATTACTTTCCTTATGTCTATTACAACATCAGCCTTGG
ATTTCTTGACTAA

Alignment

ORF - retro_shar_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.36 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEFWLISAPGDKENLQALERMNTVTSKSNLSHNTKFAIPDFKVGTLDSLVGLSDELGKLRNFHPSLIKKM
          SEFWL.S.PG..E.L..LE...T.TSKSNLS.NT.F.IPDFKVGTLDSL..LSDELG.L..F..SL.KKM
Retrocopy SEFWLVSIPGNREDLEILEQVLTFTSKSNLSLNTDFEIPDFKVGTLDSLISLSDELGRLDPFAESLMKKM

Parental  AQCVVEVMEDTKGKVYENLLANGVDLTSFVTRFEWDMAKYPAKQPLVVVVDTLAKQLAQIETDLKARTAA
          .QCV.EV.E..KG.V.E.LLA.GV.L.SFVT.FEWD..KYP.KQPL..VV..L.KQL.Q.ETDLK.R..A
Retrocopy TQCVIEVTEAKKGEVQEYLLAHGVTLASFVTHFEWDLIKYPVKQPLGEVVEALRKQLTQVETDLKTRISA

Parental  YNTLKGNLENLEKKSTGNLFTRTLADIVNKEDFVLDSEYLITLLVIVPKPNYSQWQKRYESLSDMVVPRS
          Y..LK.NLE..EKK..G.L.TR.L.DIV.KEDFVLDS.YL.TLLVIVPK..Y..WQK.YESLSDMVVPRS
Retrocopy YKKLKRNLETMEKKLLGGLLTRSLSDIVSKEDFVLDSKYLVTLLVIVPKTSYPLWQKTYESLSDMVVPRS

Parental  TKLIAEDDEGGLFTVTMFRKVINDFKAKAKENKFIVREFFYDEKEIKSEREEMTKLLSEKKQQYQTSRVA
          TKLIAED.E.GLFTVTMF.KVI.DFK.KA..NKF.VR.FFYDEKEI.SEREE.TKLL..KKQQ....R..
Retrocopy TKLIAEDNESGLFTVTMFQKVIEDFKIKATANKFKVRDFFYDEKEIESEREEITKLLAAKKQQ-ESFRKI

Parental  LKKRSSTFPDQMVK----MTPIGNPSRPSTGQTDKEKENEGEG--EGPLLRWLKVNFSEAFIAWIHLKAL
          .KK.S....D..VK......P......P.......E.E.EGEG..E.P.L.WLK..F.E.FI...H.K.L
Retrocopy QKKQSFSLLDLFVKAFTSVIPRRYQKQPKAKAQENEREAEGEGYWENPYLQWLKACFGEVFIILLHIKTL

Parental  RVFVESVLRYGLPVNFQAVLLQPHKKATKRLREVLNSVFKHLDEVAAASILDASVDIPGLQLNNQDYFPY
          RVF.ESVLRYGLPVNF.AVLLQP.KK..KRLRE.LNS.FKHLDEV.AASI.D.S.DIPGLQL.NQDYFPY
Retrocopy RVFSESVLRYGLPVNFKAVLLQPQKKSSKRLREALNSAFKHLDEV-AASIMDISLDIPGLQLGNQDYFPY

Parental  VYFHIDLSLLD
          VY..I.L..LD
Retrocopy VYYNISLGFLD

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_33 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001927	1 retrocopy	retro_btau_1823,
Callithrix jacchus	ENSCJAG00000006660	2 retrocopies	retro_cjac_1089, retro_cjac_3461,
Monodelphis domestica	ENSMODG00000014803	1 retrocopy	retro_mdom_2006,
Otolemur garnettii	ENSOGAG00000009748	1 retrocopy	retro_ogar_403,
Sarcophilus harrisii	ENSSHAG00000009886	1 retrocopy	retro_shar_33 ,
Sarcophilus harrisii	ENSSHAG00000018681	1 retrocopy	retro_shar_89,