RetrogeneDB ID: retro_shar_583

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850505.1:63504..64139(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000001147
• Aliases: None
• Description: None

Sequence

>retro_shar_583
ATGATTTTCATCTTGCTTCTCTTAGGACCACCAGAGCATCATTTGCAGACTCTAACTATGCCTCAGTGGTTTTTCAGTTT
CCAGATTTGGGGTGTAGTCTGCATAATGATCTTCATTGGGATATTCTTTAGCTCTTATTGGTTTCTATATTTAGCCTGGT
GGCACGTGAACAGAAACACTCTAAGAAAAAATCTGAAACAAGTTGAGTGTTGAAGCAATGGCATGCATAAAAGTCCCTGG
AAGACTACTTTCCTGTCTCTTTCAATAAGACAGAGGAGCTAGACTTAATCTAGAACTATATTGCTGGTTTCTACCCATAA
CTCATTCTGACTGCTAGAGTCTTCACTAAATTTTATGCTGAAGCTACCAGTTTTTCTTCTGTGTTTCCTGGGATCTGTTC
CCACCTGATGATGCTGACTTTATGAGTATGAATTCCCATCTTCAGAGATTATATTATGACTGGAGGTCAAGTGAACTCAG
GGATGGAATATATTTCATACTTGCTGAGCAAGAAGGAAAGTGGAAACTTTTTTATGTTCATTGTGGGAGGGGTCTAGGAG
ATCCTGGAGGCTCAACCTGGAAGTTATACTTTACTACTCAGAAACCAGAAAAGATTTATTAGACTTGAACAGCTC

Alignment

ORF - retro_shar_583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.94 %
• Parental protein coverage: 64.37 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MISFAPLSVPLERRLQTLAVVQWVFSFLILGIICIAIFIGLFFTRFWFLSMLYSVWWYLDRDTPRKGGRQ
          MI....L..P.E..LQTL...QW.FSF.I.G..CI.IFIG.FF...WF...LY..WW...R.T.RK...Q
Retrocopy MIFILLLLGPPEHHLQTLTMPQWFFSFQIWGVVCIMIFIGIFFSSYWF---LYLAWWHVNRNTLRKNLKQ

Parental  IQ-FIKRWRVWKYLADYFPVSLIKTVDLDPTQNYIAGFHPHGVLAAGPFINFCTEATNFSSLFPGIRSHL
          .....K.W...K.L.DYFPVS..KT..LD...NYIAGF.P...L.A..F..F..EAT.FSS.FPGI.SHL
Retrocopy VE<VLKQWHA*KSLEDYFPVSFNKTEELDLI*NYIAGFYP*LILTARVFTKFYAEATSFSSVFPGICSHL

Parental  MMLTLWFRIPIFRDYILTGGLVTSEKECVSYLLSKKEGGNLLVVIVGGAQEALDARPGNYTLLLRNRKGF
          MMLTL...IPIFRDYI.TGG.V.S..E..SYLLSKKE.GN....IVGG..E.L.A.PG.YTLLLRN.K.F
Retrocopy MMLTL*V*IPIFRDYIMTGGQVNSGMEYISYLLSKKESGNFFMFIVGGV*EILEAQPGSYTLLLRNQKRF

Parental  VRLALL
          .RL..L
Retrocopy IRLEQL

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_583 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001166	1 retrocopy	retro_meug_442,
Monodelphis domestica	ENSMODG00000006756	3 retrocopies	retro_mdom_126, retro_mdom_1269, retro_mdom_712,
Sarcophilus harrisii	ENSSHAG00000001147	1 retrocopy	retro_shar_583 ,