RetrogeneDB ID: retro_shar_514

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849743.1:296105..296484(+)
• Located in intron of: ENSSHAG00000005747

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNTTIP1
• Ensembl ID: ENSSHAG00000002289
• Aliases: None
• Description: deoxynucleotidyltransferase, terminal, interacting protein 1 [Source:HGNC Symbol;Acc:16160]

Sequence

>retro_shar_514
TTCTTTCAGAAAGCAGCATTTAATGTCAGAGACAATGACGGGGAAGGTGTTGACGCAGAGCAACTGATCCGGGAAGCTTG
CCGAAGTTGTCTGGAACAGGTTAAGCTGCTGCTTTTGGAGGGGGAGAAAGTGATATCCAGACCGACTCATGAACTTCCTG
GGATGAATCATGGCAGACAAGCAAAGGAGGGATGTTCCCCTTCGTGGAAGCCCCTTCCCAGAAAAGAGGAAGGGATGGCC
TCCGGGACACATCCTTCCAAATGACAGATTGACTTCCAACATGGTATAGAACCCAAAATCCTGGGGACCAGTTCAGAGGG
AGGGTCCTAAGTGGGATCCAGCTCAGCTGAATGAATCCACCACCTTCGTGCCTGGGGCA

Alignment

ORF - retro_shar_514 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.59 %
• Parental protein coverage: 52.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FFQKAAFNVRDNVGEDVDAEQLIQEACRSCLEQAKLLFSDGEKVIPRLTHELPGMKRGRQADEECAH-RG
          FFQKAAFNVRDN.GE.VDAEQLI.EACRSCLEQ.KLL...GEKVI.R.THELPGM..GRQA.E.C...RG
Retrocopy FFQKAAFNVRDNDGEGVDAEQLIREACRSCLEQVKLLLLEGEKVISRPTHELPGMNHGRQAKEGCSP>RG

Parental  SPIPKKRKGRPPGHILSNDRSTSGMVWKPKSCEPIRREGPKWDPARLNESTTFVLGS
          SP.P.KRKG.PPGHIL.NDR.TS.MV..PKS..P..REGPKWDPA.LNESTTFV.G.
Retrocopy SPFPEKRKGWPPGHILPNDRLTSNMV*NPKSWGPVQREGPKWDPAQLNESTTFVPGA

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_514 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000017299	1 retrocopy	retro_mmus_2387,
Pteropus vampyrus	ENSPVAG00000000368	1 retrocopy	retro_pvam_1217,
Sarcophilus harrisii	ENSSHAG00000002289	1 retrocopy	retro_shar_514 ,