RetrogeneDB ID: retro_shar_291

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841239.1:2029840..2031847(+)
• Located in intron of: ENSSHAG00000015448

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000005804
• Aliases: None
• Description: None

Sequence

>retro_shar_291
TTCATTCCTGAGAATGAAGACCTCATCTATAACCAATGGGAAGACAACATTATTTGGGATGCGCAAGGCATGCATAAGCC
ATTGTATCCTATAGTCCTAACTATTGATCCAAATGATGAGAACCTCCTGCTTTTTGATCTTGAAGAGCCTCAAGAAGAGT
CTCCAACCCCTCACCCCTTGGCCAAGAAGCACTTTTCTAAGAAGAGCCAAGTCATGAAAAGATTGGACATTGTTGGAATG
GATAAAGCTGAGCAGGCTCCTGCCCAACTGAAAACCAAGGACCCTTGGAACCTGTCCAATGATGAATTTTACTTCCCCCA
GCAGCATGGCCTCCAAGCATCCTTTGTGAACCCTAGAATCCAGCATTCAATTCCAGCACTAAAGCTACACTCCAGCCTCT
TTCCTACTCACATGAAAGCTGAGCAACTCTGTCAGTTCCATCGACCACCAGTCAGGTGGCTAGGCAAAGGCTCGCATCCT
GTCCACGACTTGACTTTCCACATCCAAAAGAAAGCCCAGGAACGAGAGCAAGAGCTTCAGGCTTCAGGGGGAGGTCACAT
GTTTTTTATGAAGACATTCCAGGACTTGAGTGGGCAGGATGGAGATCTCATTCTGGTGGAATGGAGTGAAGAGAATCCAC
CACTCTTAAATCAGGTTGGAATGGCCTCCCAGATCCAGAACTATTACAAAAGGAAAACTGGGAACAACACTGGACCTCCT
GACTATAAATATGGGAATCCTGTTTTCTGTTCATCTTCACCCTTCCTAGGGCAACTTCATGCGGGACAGTCCTTACAGGC
TTTGGAAAACAAACTATTCCGGGCTCCCATCTACCTACATCAGATGGCAGACACAGACTTTCTGGTTGTGGTGACCAAAG
CAGGCTACTTTCTTCGGGAAGTGAAAGATATATTTACCGCTGGGCAGCAGTGTCCACTGTATGAAGTTCCTGTCCCCAAG
TCAAAAATGGCAATGAATTACATTCATGATTTTCTCCAAGTGTTTATATATAGACAATTTAGGAAAAGCCCTCACAGACC
TCGGAGAATTCTTATGGAGGATATCCGCAGGGCCTTTCCTAGACTTGCTGAGAGAACTATCCAAAGGAAGCTCACCAAAT
GCTCAGAGTTCCATCGGACAGGAACCTATTTTAATTGGTGGGTGCTGAAGCCTAGATTCCGCTTGCCAAGTGAAGAGGAG
CTGAGGGACATGGTAACCCCAGAGCAATGCTGTGCTTTGTATAGTATGTTGGCTGCCCAGCAACGCCTTAAGGATGCTGT
CTGTGGGGAAGTATTGCTCCTAAACACAGAGGAGACCAGTGATCAAAACGTATGTCTCAGTGATGAGGTCCAGGCTGCTC
CATGGAACACAACTCGGGCCTTCCTAGCAGCCACAAAAGGGCAGTGTCTCCTGGAAGTGTCAGGAGCAGCTGACCCCACA
GGCTGTGGGGAGGGCATCTCCTATGTCAAAGTGGCTTGTAAACCCAAGCAGGAAGACAAAACCCAAGTGAATGGAAGGAG
AGTGAAGGGTACTGATGCAGACCTTCGACATCTCACCCTCAAGAAAGCCAAGAACTTGCTGAGAACATTTGGGATGTCAG
AGACAGAGATCAGGAAGCTATCCCGCTGGGACATGATCTCAGCTGTCCGAGCCCTGTCTACCAAGGAGCTACATTCAGGA
AACAAGTCCAGAGCCCTCACCAGATTTGCACGAGTATCCCATTCTTCAGGAGCTGAGCAGCAGAGACACTATCAGCAAGA
GGTCCAAAGAATTTTTGACCTTCAGAACAGGGTCCTGGCTTCTACCGAGGTGCTGTCCACAGATACAGATAGTAGCAGCT
CAGAAGAGGAAAATGATGAAATGATGGACTGGATGTGTCAGGGAATTGAGAACCTCCTGGAGGGTAAGACCAACTCTCGG
AGTCTACAGAGAAAAAAAGAAAAACAGGATTATCAGGAGCTGAAGCAACTGATGCTCAGAGATGGGCGTACTCACCTCCA
AGACAAA

Alignment

ORF - retro_shar_291 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.51 %
• Parental protein coverage: 77.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FIPENEDLIYGQWEDNIIWDAQAMTKPLYPTVLTLDEDDENLLLVDITEPVEAETPAPKSLTPKGSSTKN
          FIPENEDLIY.QWEDNIIWDAQ.M.KPLYP.VLT.D..DENLLL.D..EP.E.E.P.P..L..K..S.K.
Retrocopy FIPENEDLIYNQWEDNIIWDAQGMHKPLYPIVLTIDPNDENLLLFDLEEPQE-ESPTPHPLAKKHFSKKS

Parental  QLMLKCGIMEMDEAEQPPVQLKAKDPWNLSNDEFYFPQQHGLEISFRIPMVQHSIPALKLHSSLFPTHMG
          Q.M....I..MD.AEQ.P.QLK.KDPWNLSNDEFYFPQQHGL..SF..P..QHSIPALKLHSSLFPTHM.
Retrocopy QVMKRLDIVGMDKAEQAPAQLKTKDPWNLSNDEFYFPQQHGLQASFVNPRIQHSIPALKLHSSLFPTHMK

Parental  AEQLRQFHRPPLKWPGRGPQPVRSLTHYIQKKAQERLQELKASGGGHMFFMKTIQDLSGKDGDLILVEWS
          AEQL.QFHRPP..W.G.G..PV..LT..IQKKAQER.QEL.ASGGGHMFFMKT.QDLSG.DGDLILVEWS
Retrocopy AEQLCQFHRPPVRWLGKGSHPVHDLTFHIQKKAQEREQELQASGGGHMFFMKTFQDLSGQDGDLILVEWS

Parental  EENPPFMNQVGMASHIQNYYKRKIGKDTGPPAYKYGNLVFCSSSPFLGKFHPGQFLQAIENKLFRAPIYP
          EENPP..NQVGMAS.IQNYYKRK.G..TGPP.YKYGN.VFCSSSPFLG..H.GQ.LQA.ENKLFRAPIY.
Retrocopy EENPPLLNQVGMASQIQNYYKRKTGNNTGPPDYKYGNPVFCSSSPFLGQLHAGQSLQALENKLFRAPIYL

Parental  HQMADTDFLVVVTKEGCFLREVKDIFIVGQQCPLDEVPAPNSKMAKDYIHGFLQVFVYRQFWASPFRPRR
          HQMADTDFLVVVTK.G.FLREVKDIF..GQQCPL.EVP.P.SKMA..YIH.FLQVF.YRQF..SP.RPRR
Retrocopy HQMADTDFLVVVTKAGYFLREVKDIFTAGQQCPLYEVPVPKSKMAMNYIHDFLQVFIYRQFRKSPHRPRR

Parental  IRMEHIRQAFPKLAESSIRRRLTKCADFHRTGLYFNWWVLKPGFRLPSEEELRVMMTPEKCCALYSMLAA
          I.ME.IR.AFP.LAE..I.R.LTKC..FHRTG.YFNWWVLKP.FRLPSEEELR.M.TPE.CCALYSMLAA
Retrocopy ILMEDIRRAFPRLAERTIQRKLTKCSEFHRTGTYFNWWVLKPRFRLPSEEELRDMVTPEQCCALYSMLAA

Parental  QQRLKDAGYGAVSLLATEENSTEGAGLEDEVRAAPWNTTRAFLAATKGQCLLEGTGAADPTGCGEGISYV
          QQRLKDA..G.V.LL.TEE.S.....L.DEV.AAPWNTTRAFLAATKGQCLLE..GAADPTGCGEGISYV
Retrocopy QQRLKDAVCGEVLLLNTEETSDQNVCLSDEVQAAPWNTTRAFLAATKGQCLLEVSGAADPTGCGEGISYV

Parental  RLKPDLPLQQENKVRLEGARLMGTDADLRRLTLKKAQKLLRVFGVSEEEIRKLSRWEVIAAVRALSTKEL
          ......P.Q...K....G.R..GTDADLR.LTLKKA..LLR.FG.SE.EIRKLSRW..I.AVRALSTKEL
Retrocopy KVACK-PKQED-KTQVNGRRVKGTDADLRHLTLKKAKNLLRTFGMSETEIRKLSRWDMISAVRALSTKEL

Parental  NSGANSRDLTKFARTSQSSAAEQQRHFQQEVQRVFDLQNRVLASTDVLSTDTDSETSDEENAHMLDNMCH
          .SG..SR.LT.FAR.S.SS.AEQQRH.QQEVQR.FDLQNRVLAST.VLSTDTDS..S.EEN..M.D.MC.
Retrocopy HSGNKSRALTRFARVSHSSGAEQQRHYQQEVQRIFDLQNRVLASTEVLSTDTDSSSSEEENDEMMDWMCQ

Parental  EIEDLLEGKTNPQKLQRQKEKQEYQELQQLLLGHGGAPPQEK
          .IE.LLEGKTN...LQ.....Q.YQEL.QL.L..G....Q.K
Retrocopy GIENLLEGKTNSRSLQXXXXXQDYQELKQLMLRDGRTHLQDK

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_291 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
Homo sapiens	ENSG00000147133	1 retrocopy	retro_hsap_66,
Myotis lucifugus	ENSMLUG00000009092	1 retrocopy	retro_mluc_793,
Macaca mulatta	ENSMMUG00000005663	1 retrocopy	retro_mmul_1149,
Pongo abelii	ENSPPYG00000020453	1 retrocopy	retro_pabe_161,
Sarcophilus harrisii	ENSSHAG00000005804	1 retrocopy	retro_shar_291 ,