RetrogeneDB ID: retro_shar_58

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867608.1:17429..19394(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000001778
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000006407
• Aliases: None
• Description: None

Sequence

>retro_shar_58
ATGACGGAACAGAGTAAACCGGAAGGCAAGTTTAAAGCCAAGTCCGAATACAAGTCTTACGGTGAGCACGCTAGTTCGAG
TGGTGGTCCGGGCGGCGGCGGCGGCGGCGGCCCTGCAGGTGGAGGCGGCGGCAGCGGCGAGAGCAGCGGAGGGCCTCTTC
GTCAACGGGGGAGAGGTGCCTTCCGCTGGAAGAAATACCCAGAAGGGAAGTGTGGCCTCGTGAGCCAAGGCTTCAGCCGG
GCTGCGTCCTTGGACCTTCAGGGCAAGGAAGAGACCAGTGAAGGCCAAGAGGTTTCCAGAAGCAGGTACTCCCCAAATAC
CTCCCGATTCGGCAGAGACAGATGGTGGGAGCGGGGCGGAGACCGAATCCGTGTTACCGTGAGGCGGCAAGATCGAGACA
GACCGATCCTAGATCGAGGGGTGATTGTTTCCAGCCTGAGCCCGCCTTCAAAACAATGGTTCAAGGTCACAATTCCCAAT
GGCAAAAAATATGACAAAACATGGCTGTTAAATACAATTCAGAGCAAATGTAGCGTTCCCTTCGATGCGATCGAATTTCA
CTATGAAAACAACAGGGCCAATTTTTTTGTGGAGGATGCCAAAACTGCTGCTGCACTGAAAGCCGCTAACCATATCACAG
ATGATACTAACCGCAGAATCTCGATAATAATTAGTTCATCGAGCCCACCTTATTCAGTGCAAAATGAATTGAAGCCCGAA
CAGGTGGAACAGTTGAAGAATATAATGAGCAAGAAATATGATAGTTTCCAGAAATCTCTTGACCTAAAGGGACTTCGCTC
AGATCCAGATCTCATGGCTCAAAATATAGATATCGTTTTGAATCGCAAAAATTACATGTCTGCATCAATTCGAATCATTG
GGGAAAACATTCCAGATCTCTTATCGTTGAATCTGAGTAAGAATAGACTTTACAAACTAGATGACTTGTCCGAGATAATG
CCAAAGGCACCTAATCTCAAAATTCTCGACCTCTCAGACAATGAATTAAAGTCTGAACGGGAGCTTGATAAACTGAAGGG
ATTTAAGTTAGATGAACTTTGGCTCCAGGGAAATCCCCTGTGTGAAGCCTTCCAAGATCGGTCCTCCTACCTCAGTGCCA
TCCGGGAACGTTTCCCAAAGTTGTTACGTCTGGATGGCCACGAGCTGCCTCCTCCCATTGCCTTTGACGTGGAACGGTCC
CTTACACTACCTATCTGCAAGGGTAGCTACTTCGGATCAGAAACCATGAAGAACATGGTCATGTATTTCCTACAACAGTA
TTTTAACGTCTACGACACCGGCAACAGGCAGGGACTGCTGGATGCTTACCATGAGGACGCCTGCTGTTCGTTAAGTCTTC
CAGTGAGCCTTCAGAATCTATCTCGTTATAACTTGAGTGAATATGTGAATGAGAACAGAAATATGAAAAAAGTCAAAGAT
CCCAACCTGCGATACCGCCTTCTAAAACACTCCCGCCTCACCGTTGTGGCTTTTCTCAATGGATTGCCAAAGACCCAGCA
TGATATAAATTCCTTTGTGGTAGACGTTACTGCCCAGACAGAGACTTTGCTGTGTTTTTCTGTAAACGGGGTCTTTAAGG
AACTAGATGAGAAAGCCCATGATACCATTAGAGCATTCACCAGAGTATTCATTGCTGTCCCTTCAAATAATGCTACAAGG
ATGTGTATGGTGAATGACGAGCTGTTTGTAAGAAATGCCAACTCAGAAGAAATCCGTCATGCTTTTGCCCAACCGGCCCC
ACTTACACTTTCCCCAAGCTGGATGACCACCGTTTCCCAACAACAACGAGATATGTTACAGTCCTTTTCTACTCAATCTG
GTATGAATCTGGAATGGTCACAGAAATGCCTGCAAGACAACAACTGGGACTTTATTCAAGCAGCACAGATCTTTACACAG
CTCAAGGAACAAGGCAAGATTCCTGCAATAGCATTTCAAAAATGA

Alignment

ORF - retro_shar_58 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.63 %
• Parental protein coverage: 90.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDVAMSDAQDGPRSRYAPYNSRPNRRGGDNWHDR--DRIHVTVR---RDRPGQDRGSTPGSSLDAASKNW
          G....S..Q...RSRY.P..S...R.G.D.W..R..DRI.VTVR...RDRP..DRG....SSL...SK.W
Retrocopy GKEETSEGQEVSRSRYSPNTS---RFGRDRWWERGGDRIRVTVRRQDRDRPILDRGVIV-SSLSPPSKQW

Parental  FRITIPYGRKYDKTWLLNSIQSKCNVPFNPVEFHYENTRAQFFVEDASTASAIKAVNHKILDRENRRISV
          F..TIP.G.KYDKTWLLN.IQSKC.VPF...EFHYEN.RA.FFVEDA.TA.A.KA.NH.I.D..NRRIS.
Retrocopy FKVTIPNGKKYDKTWLLNTIQSKCSVPFDAIEFHYENNRANFFVEDAKTAAALKAANH-ITDDTNRRISI

Parental  IINPSAPPQSVQNELKPEQVEQLKFVMSKRYDGSQQALDLKGLRTDPDLVAQNIDVILNRRNCMSAALRI
          II..S.PP.SVQNELKPEQVEQLK..MSK.YD..Q..LDLKGLR.DPDL.AQNID..LNR.N.MSA..RI
Retrocopy IISSSSPPYSVQNELKPEQVEQLKNIMSKKYDSFQKSLDLKGLRSDPDLMAQNIDIVLNRKNYMSASIRI

Parental  IEENIPELLSLNLSNNRLYRLDDFSEIVQKAPNLKILNLSGNELKSERELDKVKRLKLDELWLVGNPLCD
          I.ENIP.LLSLNLS.NRLY.LDD.SEI..KAPNLKIL.LS.NELKSERELDK.K..KLDELWL.GNPLC.
Retrocopy IGENIPDLLSLNLSKNRLYKLDDLSEIMPKAPNLKILDLSDNELKSERELDKLKGFKLDELWLQGNPLCE

Parental  AFRDQSSYISAIREHFPKLLRLDGHELPPPIAFDVEAPTTLPPCKGSYFGSENLKAMVLYFLQQYYSVYD
          AF.D.SSY.SAIRE.FPKLLRLDGHELPPPIAFDVE...TLP.CKGSYFGSE..K.MV.YFLQQY..VYD
Retrocopy AFQDRSSYLSAIRERFPKLLRLDGHELPPPIAFDVERSLTLPICKGSYFGSETMKNMVMYFLQQYFNVYD

Parental  SGDRQGLLDAYHDQACCSLSIPFTIQNPSRGNMSEYFKDSRNVKKLKDPTLRFRLLKHTRLNVVAFLNEL
          .G.RQGLLDAYH..ACCSLS.P...QN.SR.N.SEY....RN.KK.KDP.LR.RLLKH.RL.VVAFLN.L
Retrocopy TGNRQGLLDAYHEDACCSLSLPVSLQNLSRYNLSEYVNENRNMKKVKDPNLRYRLLKHSRLTVVAFLNGL

Parental  PKTQHDVNSFVVDICAQTETLLCFAVHGVFKEVDGKSRDSVRAFSRVFIAVPSNNAARLCIVNDKLFIRN
          PKTQHD.NSFVVD..AQTETLLCF.V.GVFKE.D.K..D..RAF.RVFIAVPSNNA.R.C.VND.LF.RN
Retrocopy PKTQHDINSFVVDVTAQTETLLCFSVNGVFKELDEKAHDTIRAFTRVFIAVPSNNATRMCMVNDELFVRN

Parental  ATTDEIRRAFAMPAP-TPSSSPVPTLSPEQQEMLQTFSTQSGMNLEWSQKCLQDNDWDFARAAQVFTQLK
          A...EIR.AFA.PAP.T.S.S...T.S..Q..MLQ.FSTQSGMNLEWSQKCLQDN.WDF..AAQ.FTQLK
Retrocopy ANSEEIRHAFAQPAPLTLSPSWMTTVSQQQRDMLQSFSTQSGMNLEWSQKCLQDNNWDFIQAAQIFTQLK

Parental  AGGKIPEVAFLK
          ..GKIP..AF.K
Retrocopy EQGKIPAIAFQK

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_58 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000010798	1 retrocopy	retro_mmur_243,
Otolemur garnettii	ENSOGAG00000002202	1 retrocopy	retro_ogar_1174,
Sarcophilus harrisii	ENSSHAG00000006407	1 retrocopy	retro_shar_58 ,
Ictidomys tridecemlineatus	ENSSTOG00000010889	1 retrocopy	retro_itri_615,