RetrogeneDB ID: retro_shar_245

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834796.1:1415593..1416191(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000013051
• Aliases: None
• Description: None

Sequence

>retro_shar_245
AGTTTTGTCCAAAATATGATAAGCCCTGATCAATGAACAGAGCAGACAAAAGAATGTAAAACATGGAGACCCCAAAATGA
AGCCAAAAAAAGACCCCATGAATCACCCGATGAAGAGAAAGAGCCTTGCTCAAAACTTGCAAAACAAAATACAGACAGTA
CCTTTTCTTAGCAAATGATATTTTCTTATATGGGAGATGCAGCCATGGTTTACAGAAATGGCTGCTGCTCCAGCAATGGG
AAGGGGAAAGCTCAAGCTGGCATTGGTGTTTACTGGGGACCAGGACACCCCCTAAATGTGGGTGATAGACTTCCTGGGCA
ACAAGTAACCAAACTGCAGAAATCCATGCTCCCTGTAAAGCAATTGAACAATCCAAGAATCAAAACATCAGTAAGCTGGT
TCTCTCCCCAGTTAGTATGTTTTAATATAAAATGGTATTGCAATTTGGGTTAAAGAGTGGAAGAAAAATGGCTGGACAAC
AAGCACAGGAAAAGATGTCATTAATAAGGAAGACTTTGTTAAGCCTGATACACTTATTCAAGGCATAAAGTTAACATGGG
TGTATGTTTCCAGTCATTCAGGATTTTCAGGCAAGAAG

Alignment

ORF - retro_shar_245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.68 %
• Parental protein coverage: 68.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AFVRNT-SPDHSTEQKKECNTQ-DHKMKPKK-RPCESSDEEEDPCSKLAKQNTDSIPSLSKNIFSYMGDA
          .FV.N..SPD..TEQ.KEC.T..D.KMKPKK.RP.ES.DEE..PCSKLAKQNTDS..S....IFSYMGDA
Retrocopy SFVQNMISPDQ*TEQTKECKTW>DPKMKPKK<RPHESPDEEKEPCSKLAKQNTDSTFS*QM-IFSYMGDA

Parental  AVVYTDGCCSSNGRRKARAGIGVYWGPGHPLNVGDRLPGRQ-TNQRAEIHAACKAIEQAKNQNISKLVLY
          A.VY..GCCSSNG..KA.AGIGVYWGPGHPLNVGDRLPG.Q..NQ.AEIHA.CKAIEQ.KNQNISKLVL.
Retrocopy AMVYRNGCCSSNGKGKAQAGIGVYWGPGHPLNVGDRLPGQQ<SNQTAEIHAPCKAIEQSKNQNISKLVLS

Parental  TDSM-FTI-NGITSWVKDWKKNGWKTSTGKEVINKEDFVKLDTLIQGIDIKWIHVPGHSGFAGNE
          ..SM.F.I.NGI..WVK.WKKNGW.TSTGK.VINKEDFVK.DTLIQGI...W..V..HSGF.G..
Retrocopy PVSM>FNI>NGIAIWVKEWKKNGWTTSTGKDVINKEDFVKPDTLIQGIKLTWVYVSSHSGFSGKK

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_245 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 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008547	6 retrocopies	retro_chof_158, retro_chof_1653, retro_chof_1836, retro_chof_2224, retro_chof_485, retro_chof_843,
Callithrix jacchus	ENSCJAG00000035450	1 retrocopy	retro_cjac_3811,
Echinops telfairi	ENSETEG00000012674	1 retrocopy	retro_etel_1286,
Homo sapiens	ENSG00000171865	2 retrocopies	retro_hsap_1814, retro_hsap_300,
Gorilla gorilla	ENSGGOG00000034822	2 retrocopies	retro_ggor_2175, retro_ggor_336,
Macropus eugenii	ENSMEUG00000003610	1 retrocopy	retro_meug_1172,
Macaca mulatta	ENSMMUG00000014475	2 retrocopies	retro_mmul_544, retro_mmul_799,
Monodelphis domestica	ENSMODG00000014491	1 retrocopy	retro_mdom_593,
Nomascus leucogenys	ENSNLEG00000015400	2 retrocopies	retro_nleu_2399, retro_nleu_2959,
Pongo abelii	ENSPPYG00000025873	1 retrocopy	retro_pabe_18,
Pan troglodytes	ENSPTRG00000011614	1 retrocopy	retro_ptro_244,
Pteropus vampyrus	ENSPVAG00000002070	1 retrocopy	retro_pvam_144,
Sarcophilus harrisii	ENSSHAG00000013051	1 retrocopy	retro_shar_245 ,