RetrogeneDB ID: retro_shar_193

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834603.1:3547801..3548209(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF114
• Ensembl ID: ENSSHAG00000001827
• Aliases: None
• Description: ring finger protein 114 [Source:HGNC Symbol;Acc:13094]

Sequence

>retro_shar_193
TTGTCTCCAGGAATTAGAGCCATGGACTTAGAAAAGCAAATTGAAGCAATTGGGGCAAATTTTAGTAGTTGTAATAAAAA
TCTGGTCCTTTCAAAAATGCATAACTATGTGACTTCCTGTTCCAAGTATCAAAGCTACTAATGGATAGTGTTAAGTGTTA
AATCTACCTACCACTAAAGATACAGCACATCAGCCAAGAAATCACCAAATCAATTCACCTTTCCTTGTTTTTTATGATCA
TGAGAAAATTTTTATCAGGAAGATCTAGATAAATACTACAAAATATGCCACAGCACAGATACTTAATTTGTCCAAATTGT
CTCTCAGTGCCTTTGGGAGTTCCCAATTACCAGAGTACTAACTTCATGGATCACATTCAGCTGCAAACATCAGTTGTCCT
ATGACACT

Alignment

ORF - retro_shar_193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.43 %
• Parental protein coverage: 58.87 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSLGTKAVDLEKQIEATEATCSGCKKKLALSKMRNHVASCSKYQSY--LMEGVKATTKDMTYQPSRNIPN
          LS.G..A.DLEKQIEA..A..S.C.K.L.LSKM.N.V.SCSKYQSY......VK.T............PN
Retrocopy LSPGIRAMDLEKQIEAIGANFSSCNKNLVLSKMHNYVTSCSKYQSY*WIVLSVKSTYH*RYSTSAKKSPN

Parental  RFTFPCPYCPEKNFDQEGLAEHCKMYHSTDTKSVVCPICASMPWGDP-NYRSANFMDHIQR-RHQFSYDT
          .FTFPC......NF.QE.L....K..HSTDT..V...I.....W..P.NY.S.NFMDHIQ...HQ.SYDT
Retrocopy QFTFPCFL*S*ENFYQEDLDKYYKICHSTDT*FV--QIVSQCLWEFP<NYQSTNFMDHIQL>KHQLSYDT

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_193 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 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009113	2 retrocopies	retro_dnov_1534, retro_dnov_1557,
Microcebus murinus	ENSMICG00000011155	1 retrocopy	retro_mmur_992,
Otolemur garnettii	ENSOGAG00000003953	3 retrocopies	retro_ogar_1149, retro_ogar_2158, retro_ogar_2330,
Ochotona princeps	ENSOPRG00000004732	2 retrocopies	retro_opri_368, retro_opri_709,
Pteropus vampyrus	ENSPVAG00000004117	4 retrocopies	retro_pvam_1136, retro_pvam_1148, retro_pvam_1149, retro_pvam_1477,
Sarcophilus harrisii	ENSSHAG00000001827	1 retrocopy	retro_shar_193 ,