RetrogeneDB ID: retro_shar_18

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867607.1:2726866..2727694(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000017452
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000017610
• Aliases: None
• Description: None

Sequence

>retro_shar_18
ATGGCTCGGAAGTCCAGCCCGCAGCTGCTGGCCTGGGCCCAGACTCCTTCTCATCTGCAGTTCAACCCGTTCGTGCTGAC
AGGCTACCGGCCCTCCAGCAGCACGCTGGGCTGTGTCCTCAGCCTATTCTACCTGCACAACGAGCTGGGCAACATCTACA
TCCACGGGCTGGCCCTGCTGGTCTTCCTGGTGCTGCTGCCCCTGACCATCCCCTGGGGCCAGCTGGGCTGGGGCTGCTGG
CTGGGTGGCACCCATTGCTTGGCTTGCCTGGCACCCCCCGCCGGTTCTGTCCTCTACCACCTCTTCATGTGCCACCAAGG
AGGCAGCCACGTCTATACCCGCCTCCTGGCCCTCGATATGTGCGGGGTCTGGCTGGCCAACAGCCTGGGAGCCTTACCCA
TGATTCACTCCACCCTGACCTGCTGGCCTCGCCTGCGCCTGGTCATCCTGCTGCTTTACACCTTGCTATCCATCAAAGCC
GGCTGGCATGCCGTCACCGCCCGCTCGAATATGGCTCGGCTCCAGGCCTTCGGCTGGCAGGCCATCACCCGCCTGCTGGT
GTTCGGGATCCGGGCTCTGGGAGTAGGTTCCGGAGCCCCCGGGGCCTTGCCTTGCTACCTTCGAATGGATGCCTTGGCGC
TGCTGGGAGGACTGGTGAACGTGGCCCGGTTGCCAGAGAGCTGGAATCCGGGGGCTTTCGATTACTGGTGTAACTCCCAC
CAGATCATGCATGTGCTCAGTGTCATCTCCATCCTCCAGCTGCATGCAGGGGTGGTTCCAGACCTGCTCTGGGCTGCTAA
CCATAATTATACCTGTCCTGCAGCTTGA

Alignment

ORF - retro_shar_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.56 %
• Parental protein coverage: 99.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFLSGPRL---ASSPPHLQFNKFVLTGYRPASSGSGCLRSLFYLHNELGNIYTHGLALLGFLVLLPLTM
          MA..S.P.L...A..P.HLQFN.FVLTGYRP.SS..GC..SLFYLHNELGNIY.HGLALL.FLVLLPLT.
Retrocopy MARKSSPQLLAWAQTPSHLQFNPFVLTGYRPSSSTLGCVLSLFYLHNELGNIYIHGLALLVFLVLLPLTI

Parental  PWGQLGGGGWLGGTHCVACLAPPAGSVLYHLFMCHRGGSPVYARLLALDMCGVCLVNTLGALPIIHCTLA
          PWGQLG.G.WLGGTHC.ACLAPPAGSVLYHLFMCH.GGS.VY.RLLALDMCGV.L.N.LGALP.IH.TL.
Retrocopy PWGQLGWGCWLGGTHCLACLAPPAGSVLYHLFMCHQGGSHVYTRLLALDMCGVWLANSLGALPMIHSTLT

Parental  CRPWLRPAALVGYTLLSGLAGWRALTAPSTSARLRAFGWQAGARLLVFGARGMGLGAGAPGSLPCYLRMD
          C.P.LR...L..YTLLS..AGW.A.TA.S..ARL.AFGWQA..RLLVFG.R..G.G.GAPG.LPCYLRMD
Retrocopy CWPRLRLVILLLYTLLSIKAGWHAVTARSNMARLQAFGWQAITRLLVFGIRALGVGSGAPGALPCYLRMD

Parental  ALALLGGLVNVARLPERWGPGRFDYWGNSHQIMHLLSVGSILQLHAGVVPDLLWAARH--ACP
          ALALLGGLVNVARLPE.W.PG.FDYW.NSHQIMH.LSV.SILQLHAGVVPDLLWAA.H...CP
Retrocopy ALALLGGLVNVARLPESWNPGAFDYWCNSHQIMHVLSVISILQLHAGVVPDLLWAANHNYTCP

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_18 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001349	1 retrocopy	retro_meug_1124,
Monodelphis domestica	ENSMODG00000016528	1 retrocopy	retro_mdom_2021,
Sarcophilus harrisii	ENSSHAG00000017610	1 retrocopy	retro_shar_18 ,