RetrogeneDB ID: retro_shar_299

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841257.1:1086585..1086869(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19orf40
• Ensembl ID: ENSSHAG00000016372
• Aliases: None
• Description: chromosome 19 open reading frame 40 [Source:HGNC Symbol;Acc:28467]

Sequence

>retro_shar_299
GTGGTAGGAAGCGGCTATAGAAAAGGGCTGCTCAACTTAGAAATGCCAATAATCTTTAAGGGATTATGGTAGATGAAAAA
ACACAGATGAGTGAACAGTACTTTTTAACAATACAGAAATTTATTCTGGAACTCAGAGTGGTATGGCTTCTAATGGCCAG
ACAAATGGAAGCATTCCAGTTCATTATCCAACTGTTTGTGAACAAAATGAAGAGAGGGATAGGAATCCTTTTCTTAGGTA
TAAACCATAGTCAGTTCTCTGAATCACCAGTATCTTGAACAGTA

Alignment

ORF - retro_shar_299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.59 %
• Parental protein coverage: 53.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VAGNGYKK-RIVRLRNASNLQGIIIVEKTQMSEQYFPAVQKFVVLELGMALLPVSSQMEASQLIIQL-VH
          V.G.GY.K.R...LRNA.NL.GI...EKTQMSEQYF...QKF..LEL....L....QMEA.Q.IIQL.V.
Retrocopy VVGSGYRK<RAAQLRNANNL*GIMVDEKTQMSEQYFLTIQKF-ILELRVVWLLMARQMEAFQFIIQL<VC

Parental  EQTKERNRNPFLRKK-NCQLSESSVLQTI
          EQ..ER.RNPFLR.K...Q.SES.V..T.
Retrocopy EQNEERDRNPFLRYK>HSQFSESPVS*TV

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_299 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 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000728	2 retrocopies	retro_cjac_1011, retro_cjac_3952,
Cavia porcellus	ENSCPOG00000011965	1 retrocopy	retro_cpor_1536,
Dasypus novemcinctus	ENSDNOG00000014134	4 retrocopies	retro_dnov_1817, retro_dnov_2382, retro_dnov_426, retro_dnov_942,
Echinops telfairi	ENSETEG00000002716	1 retrocopy	retro_etel_458,
Loxodonta africana	ENSLAFG00000006401	4 retrocopies	retro_lafr_165, retro_lafr_365, retro_lafr_415, retro_lafr_789,
Myotis lucifugus	ENSMLUG00000013287	1 retrocopy	retro_mluc_522,
Macaca mulatta	ENSMMUG00000017939	1 retrocopy	retro_mmul_788,
Procavia capensis	ENSPCAG00000009727	1 retrocopy	retro_pcap_444,
Sarcophilus harrisii	ENSSHAG00000016372	1 retrocopy	retro_shar_299 ,