RetrogeneDB ID: retro_shar_654

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856938.1:1846354..1847377(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTPBP4
• Ensembl ID: ENSSHAG00000014713
• Aliases: None
• Description: GTP binding protein 4 [Source:HGNC Symbol;Acc:21535]

Sequence

>retro_shar_654
ATTATCAATAGACAGAAACAGAGCCTGGACTATCTGGAACAAGTGCATCAGCATTTATTATGTCTGCCAACTATTGATTC
AAATTCCCAGACTCTGCTTCTATGTAGATATGCAAATGTTGGAAAACCCAGTTTCATTAATAAGGTGACAAGAGCATATA
TGGATGTGCAGTCTTATGCCTTTACAATCAAACCTTTGTTTGTAGGGCACATGGATTATAAATATTTGCTTTGGCAGGGG
TCAACTCTTCAGGAATTCTGAATCACTCTCTGAAAGATAGGAACCCCATTGACATGGAGGGTATAATAGCATTGGTCCAC
CTTCATGCTGCTGTGTTGTATGTCATGGATGTGTCTGAACAATGTAGTCATAATCTGGAAGAACAACTGGAACTCCTTAA
AAACATTAAGCTAATTTTTGCTAATAAGCTTCTTATAATTATGACAAATAAATGTGATGTAAAGAGGCTATCTGAACTTC
CAGAGGATGATTAAAAATATTTGTAGATTTGGAAGCTTAAAGACTTCTTGTTATAAAGAAAAGTATCCTGATTGAAGAAG
GTATTTTAAAGTTAAAACAGAGGCTTGTGATAGATTTTTGGCTCATTTAGTTGAAAGCAAAATGAAAGTAAATAATGTGC
TGAACATATTGCATTTGGCATTACCTAGTAAAAGAGATGATAAGGAGAGACCATCATTCATTACTGAAAGTATGCTAGCA
TGCAAGAAGAGAAGGGAATCTGATGCAACCAAAAAGAAGAAAGAATGAGATCTTAAGCTGGAAATGGGAGATGATTACAT
TTTGGATCTTCAGAAATATTGGGATCTAATGAATTCATTTAAAAAATATGATAAAATACCAGAAATTTGGAAAGGCCAAA
CCATAGCTGATTATATTGATTCAAACATCATGGAGAAATTGAAAGAGCTAGAGGAGGAAGAACTAAGGCAAGCTGCTTGA
GAATATGACAGTGAATCAGAAACTGAAGATGAAAAAATGATGGAAATCTATTGATTGGCAAAA

Alignment

ORF - retro_shar_654 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.21 %
• Parental protein coverage: 51.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IIKRQKQSLEYLEQVRQHLSRLPTIDPNTRTLLLCGYPNVGKSSFINKVTRADVDVQPYAFTTKSLFVGH
          II.RQKQSL.YLEQV.QHL..LPTID.N..TLLLC.Y.NVGK.SFINKVTRA..DVQ.YAFT.K.LFVGH
Retrocopy IINRQKQSLDYLEQVHQHLLCLPTIDSNSQTLLLCRYANVGKPSFINKVTRAYMDVQSYAFTIKPLFVGH

Parental  MDYRYLRWQV-VDTPGILDHPLEDRNTIEMQAITALAHLRAAVLYVMDVSEQCGHNLEEQLKLFKNIKPL
          MDY.YL.WQ..V...GIL.H.L.DRN.I.M..I.AL.HL.AAVLYVMDVSEQC.HNLEEQL.L.KNIK..
Retrocopy MDYKYLLWQG<VNSSGILNHSLKDRNPIDMEGIIALVHLHAAVLYVMDVSEQCSHNLEEQLELLKNIKLI

Parental  FANKPLIIVANKCDVKRISELPEDD-QKIFADLEAEGLPVIETSTLTEEGVIK-VKTEACDRLLTHRVET
          FANK.LII..NKCDVKR.SELPEDD..KIF.DLEA..L.VI..S.L.EEG..K.VKTEACDR.L.H.VE.
Retrocopy FANKLLIIMTNKCDVKRLSELPEDD<LKIFVDLEA*RLLVIKKSILIEEGILK<VKTEACDRFLAHLVES

Parental  KMKGNKVNDVLNRLHLAVPSKRDDKERPPFIPEGVIARKKRMEIDAPKKKRERDLELEMGDDYILDLQKY
          KM...KVN.VLN.LHLA.PSKRDDKERP.FI.E...A.KKR.E.DA.KKK.E.DL.LEMGDDYILDLQKY
Retrocopy KM---KVNNVLNILHLALPSKRDDKERPSFITESMLACKKRRESDATKKKKE*DLKLEMGDDYILDLQKY

Parental  WDLMNSSEKYDKIPEIWEGHNIADYIDPDIMEKLKELEKEEELREAAGEYDSESETEDEEMMEIHQLAK
          WDLMNS..KYDKIPEIW.G..IADYID..IMEKLKELE.EEELR.AA.EYDSESETEDE.MMEI..LAK
Retrocopy WDLMNSFKKYDKIPEIWKGQTIADYIDSNIMEKLKELE-EEELRQAA*EYDSESETEDEKMMEIY*LAK

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_654 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008494	2 retrocopies	retro_cjac_2592, retro_cjac_992,
Cavia porcellus	ENSCPOG00000013736	1 retrocopy	retro_cpor_996,
Rattus norvegicus	ENSRNOG00000016217	2 retrocopies	retro_rnor_1961, retro_rnor_2882,
Sarcophilus harrisii	ENSSHAG00000014713	1 retrocopy	retro_shar_654 ,
Ictidomys tridecemlineatus	ENSSTOG00000010042	1 retrocopy	retro_itri_1466,