RetrogeneDB ID: retro_shar_573

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850262.1:184376..184783(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000008787
• Aliases: None
• Description: None

Sequence

>retro_shar_573
CCAAATTTCAAACTGTATATCTGCCTATCTAATATGACAAATCAGAATACAAATGATTAGCTGGAGAAAATCAAACAGAA
GTTGTTTAAGAACCTTTTGTATGTTGCCTCATGCCCTGATGTACATATGCAACCAATTTCTGAAGATGAGACACAGGAAG
ACAATAGAAATGAAGAAGAGGAAGATCCTGACAAGTGCATTTCAATATCTTCTTTAGACAAGAGAATTGTATGAGAGGAG
GAGTTTTCAGACTCAGATGAGGAAGATGAGGGTGGTTGGAAAAGAAAGGCAAGAAGGTCAAAATGGAAGAGGAAAAAGAT
TGAGAGCCAGAGGAGAAAAAAGCAAAGGAGGAGGAGAATACAAAGGAAAAGAAACCTGAGACCAGAGGGATAAAGGAGGA
AACTAAG

Alignment

ORF - retro_shar_573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.2 %
• Parental protein coverage: 84.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PDFKLHISPSNMTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQPIPEDGIQEDSGDEDEEDPDKRISIC
          P.FKL.I..SNMTNQNTN..LEKIKQ.LF.NL......P.V.MQPI.ED..QED...E.EEDPDK.ISI.
Retrocopy PNFKLYICLSNMTNQNTND*LEKIKQKLFKNLLYVASCPDVHMQPISEDETQEDNRNEEEEDPDKCISIS

Parental  SSDKRIACEEEFSDSDEEGEGGRKNSSNFKKAKRVKME-EEKDREPEEKKEAKEEE-KTKEEKPEAK
          S.DKRI..EEEFSDSDEE.EGG.K......K.KR.K.E.E.......E....KE....T...K.E.K
Retrocopy SLDKRIV*EEEFSDSDEEDEGGWKRKARRSKWKRKKIE<EPEEKKAKEEENTKEKKPETRGIKEETK

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_573 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.

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Callithrix jacchus	ENSCJAG00000000970	2 retrocopies	retro_cjac_2490, retro_cjac_830,
Homo sapiens	ENSG00000116478	1 retrocopy	retro_hsap_826,
Gorilla gorilla	ENSGGOG00000011741	1 retrocopy	retro_ggor_676,
Myotis lucifugus	ENSMLUG00000013837	1 retrocopy	retro_mluc_283,
Macaca mulatta	ENSMMUG00000009948	2 retrocopies	retro_mmul_1085, retro_mmul_2518,
Mus musculus	ENSMUSG00000028800	1 retrocopy	retro_mmus_153,
Nomascus leucogenys	ENSNLEG00000002473	1 retrocopy	retro_nleu_259,
Otolemur garnettii	ENSOGAG00000005709	3 retrocopies	retro_ogar_2181, retro_ogar_3022, retro_ogar_3313,
Pelodiscus sinensis	ENSPSIG00000004134	1 retrocopy	retro_psin_44,
Pteropus vampyrus	ENSPVAG00000013325	1 retrocopy	retro_pvam_1339,
Rattus norvegicus	ENSRNOG00000009568	3 retrocopies	retro_rnor_1091, retro_rnor_1098, retro_rnor_2457,
Sarcophilus harrisii	ENSSHAG00000008787	1 retrocopy	retro_shar_573 ,
Tursiops truncatus	ENSTTRG00000001613	1 retrocopy	retro_ttru_1236,