RetrogeneDB ID: retro_shar_119

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856821.1:99360..99888(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000004322
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000002595
• Aliases: None
• Description: None

Sequence

>retro_shar_119
ATGTCCTACCAGAATCAGCAGCAGTGCAAACAGCCTTGCCAGCCACCTCCTATTTGGTCACAGCCTTGCCAGCCTAAGTG
TCCAGAGCCGTGTCCTTCTAGGTGCCCAGAGCCATGCCAGCCTAAGTGCTCTGAGCCATGTCCTCCCAGGTGTCCAGAGC
CATGCCAGCCTAAGTGCCCTGAGCCATGCCCTCCTAGGTGCCCTGAGCCATGCCAACCTAAGTGCCCTGAACCATGCCAC
CCTAAGTGCCCTGAGCCATGCCCTCCTAGGTGCCCAGAGCCATGTCCTCCTAGGTGTCCAGAGCCATGCCAGCCTAAGTG
CCCTGAGCCATGCCCTCCTAGGTGCCCTGAGCCATGCGCTCCTAGATGCCCTGAGCCATGCCAGCCTAAGTGCCCTGAGT
CATGTCCTCCTAAGTGTCCAGAGCCATGTCCTCCTAAGTGCCCTGAGCCATGCCCTCCTAGGTGCCCTGAACCATGCCCT
CCTAGGTGCCCTGAGCCATGCCCTCCTAAGTGCCCTGGGCCATGCTAG

Alignment

ORF - retro_shar_119 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.07 %
• Parental protein coverage: 99.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QQQQQGKQPCLSSPQYS---QPKCPNPCHPKNPEPCLSTCSDPCHPKYPDPCPPKYPDPCHPKSPEPPDA
          Q.QQQ.KQPC...P..S...QPKCP.PC....PEPC...CS.PC.P..P.PC.PK.P.PC.P..PEP...
Retrocopy QNQQQCKQPCQPPPIWSQPCQPKCPEPCPSRCPEPCQPKCSEPCPPRCPEPCQPKCPEPCPPRCPEP---

Parental  CHPKCPDPCHLKNPESCPPKCPDPCHSKNPEPCPPKCPDPCHSKNPEPCSPKCPDPCHPKNPEPCPSKCP
          C.PKCP.PCH.K.PE.CPP.CP.PC....PEPC.PKCP.PC....PEPC.P.CP.PC.PK.PE.CP.KCP
Retrocopy CQPKCPEPCHPKCPEPCPPRCPEPCPPRCPEPCQPKCPEPCPPRCPEPCAPRCPEPCQPKCPESCPPKCP

Parental  DPCPPKCSE
          .PCPPKC.E
Retrocopy EPCPPKCPE

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_119 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	ENSMEUG00000005041	1 retrocopy	retro_meug_3,
Sarcophilus harrisii	ENSSHAG00000000690	1 retrocopy	retro_shar_88,
Sarcophilus harrisii	ENSSHAG00000002595	1 retrocopy	retro_shar_119 ,