RetrogeneDB ID: retro_shar_459

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849566.1:43788..44349(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MARCH5
• Ensembl ID: ENSSHAG00000018432
• Aliases: None
• Description: membrane-associated ring finger (C3HC4) 5 [Source:HGNC Symbol;Acc:26025]

Sequence

>retro_shar_459
CTTGCAGATAAACTGATCTTAAAAACCTGTTTATTTGCTGTAGCAGGAATAATGATAAACTGTATCTATTAAACTGCTGG
AAATTATGGACCTCTGAAAGTAGTACAAATGATGGCCATAAGGAAGGTTTGGATGTTATAGAAAGAGCTGATCCTTTGTT
GCTTTTAATTGGATTTCCCACTATTCCTGGCATGCTGATATTAGGCAAGATGACTCATTAGGAAGACTAAATTCTTAGAT
TATGCTACAAATACTCCAATAAACTACAGATTTTGGACAATGTATTTCCAGAAGTTGGATGTCCTGTTTCTCATATTCCA
GTTGAGGAAAATCCTTTGGCAGATTATGTCTCTACTACTTTTTTGGGTAGACCTCTTGTCTTTCCCACTATTGCTGCAAT
AGCAAAAAAAAACTCATACTCAGTATTAATTCTAACCTACAAAAGAAAATCTTGGATCAAATTGCTTGTGTTGCCATAAA
AGAAACATTTAAGTTTTACTTCAAACAGCAACAATATTTACATGAAGCACACTACAAAATTTTAATTATCCAGAGGAAGA
A

Alignment

ORF - retro_shar_459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.1 %
• Parental protein coverage: 67.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LADRLISKACPFAAAGIMVGSIYWTAVTYGAVTVMQVV-GHKEGLDVMERADPLFLLIGLPTIPVMLILG
          LAD.LI.K.C.FA.AGIM...IY.TA..YG...V.Q...GHKEGLDV.ERADPL.LLIG.PTIP.MLILG
Retrocopy LADKLILKTCLFAVAGIMINCIY*TAGNYGPLKVVQMM<GHKEGLDVIERADPLLLLIGFPTIPGMLILG

Parental  KMIRWEDYVLRLWRKYSNKLQILNSIFPGIGCPVPRIPAEANPLADHVSATRILCGALVFPTIATIVGKL
          KM...ED..LRL..KYSNKLQIL...FP..GCPV..IP.E.NPLAD.VS.T..L...LVFPTIA.I....
Retrocopy KMTH*ED*ILRLCYKYSNKLQILDNVFPEVGCPVSHIPVEENPLADYVSTT-FLGRPLVFPTIAAIXXXX

Parental  MFS-SVNSNLQRTILGGIAFVAIKGAFKVYFKQQQYLRQAHRKIL-NYPEQE
          ..S.S.NSNLQ..IL..IA.VAIK..FK.YFKQQQYL..AH.KIL.NYPE.E
Retrocopy SYS<SINSNLQKKILDQIACVAIKETFKFYFKQQQYLHEAHYKIL<NYPEEE

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_459 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020981	1 retrocopy	retro_btau_1749,
Macropus eugenii	ENSMEUG00000011031	1 retrocopy	retro_meug_1192,
Mus musculus	ENSMUSG00000023307	3 retrocopies	retro_mmus_1559, retro_mmus_3211, retro_mmus_3373,
Sarcophilus harrisii	ENSSHAG00000018432	1 retrocopy	retro_shar_459 ,
Xiphophorus maculatus	ENSXMAG00000007675	1 retrocopy	retro_xmac_25,