RetrogeneDB ID: retro_shar_88

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL857608.1:27178..27685(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000002266
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000000690
• Aliases: None
• Description: None

Sequence

>retro_shar_88
ATGTCTTCCCATCAACAGAAGCAGCCCAATGTTATACCCCCTCAGCTCCAGCAGCAGCAGGTGAAACAGCCCTGCCAGCC
ACCTCCCCAGAAGCCATTTGTCCCTCATACCAAGGAGCCATGCGACCCTCAGATCCCAGGGTCAGGCACCACCAAGCTGC
CAGAGCCATGCTACCCTGAGGTTTCAGTGCCAAGCCATCCTCAAGTCCCAGGTACAGGAACCACCAAGCTGCCAGAGCCA
TGCTACCCTGAGGTCTCAATGCCAAAACAGCCTCAGGTCCCGGGGACAGGAACCACCAAGCTGCCAGAGCCATGCAACCC
TGAGGTTTCAGTGCCAAGCCATCCTCAGGTCCCAGGAACAGGAACCACCAAGCTGCCAGAGCCATGCAACCCCGAGGTTT
CAGTGCCAAGCCATCCTCAGGTCCCAGGAACAGGAACCACCAAGGTTCCAGGTCCCTATCCCACCACAATTACGCCACCT
CTTAGCCAAGAGAAGTACCCACAGGTC

Alignment

ORF - retro_shar_88 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSHQQKQPSVIPPQLQQQQVKQPCQPPPQKPFVPHTKEPCDPQVPGTGTIKVPGPQYPQVPVPSHPQVP
          MSSHQQKQP.VIPPQLQQQQVKQPCQPPPQKPFVPHTKEPCDPQ.PG.GT.K.P.P.YP.V.VPSHPQVP
Retrocopy MSSHQQKQPNVIPPQLQQQQVKQPCQPPPQKPFVPHTKEPCDPQIPGSGTTKLPEPCYPEVSVPSHPQVP

Parental  GTGTTKVPGPSCMTLKEPNDFQTKEPCHPKVPEPCYPKVPEPCHPKVPEPCHPKVPEPCHPKVPEPCHPK
          GTGTTK.P.P.......P...Q.......K.PEPC.P.V..P.HP.VP.....K.PEPC.P.V..P.HP.
Retrocopy GTGTTKLPEPCYPEVSMPKQPQVPGTGTTKLPEPCNPEVSVPSHPQVPGTGTTKLPEPCNPEVSVPSHPQ

Parental  VPEPCHPKVPEPCSTTVTLPPAQQKCPQV
          VP.....KVP.P..TT.T.P..Q.K.PQV
Retrocopy VPGTGTTKVPGPYPTTITPPLSQEKYPQV

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_88 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 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,