RetrogeneDB ID: retro_shar_124

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849794.1:75542..76067(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000003799
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000015218
• Aliases: None
• Description: None

Sequence

>retro_shar_124
CATAGTGAAACAACTAAAAAACGGGATGACTATTTAGAATGGCCTGAATACTTCATGGCTGTGGCCTTTTTATCTGCTCA
GAGGAGCAAAGATCCACATTCCCAGGTTGGGGCTTGCATCGTCAACACAGAAAACAAAATTGTTGGAATTGGGTACAATG
GGATGCCCAATGGGTGTAGTGATGACTTGCTTCCTTGGAGGAGAACGGTTGATAGTAAACTGGACACAAAATATCCTTAC
ATGTGCCATGCTGAATTGAATGCCATTATGAACAAAAATTCAGCCGATGTGAAGGGTTGTACCATGTATGTCGCCTTATT
CCCATGTAATGAATGTGCTAAACTCATCATCCAGGCAGGTATAAAAGAAGTTATTTATATGTCTGATAAATACCACGATA
GTGATGAAACCACAGCTGCAAGACTCACGTTTGACTTGGCTGGGATTAAATTCAGGAAATTCACATCCAAGTACAGCAAG
ATTGTCATTGACTTTGATTCAATTGACAGCAGACCGAGTCAAAAG

Alignment

ORF - retro_shar_124 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.43 %
• Parental protein coverage: 94.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HSETTKKRDDYLEWPEYFMAVAFLSAQRSKDPNSQVGACIINAENKIVGIGYNGMPNGCSDDLLPWRRTA
          HSETTKKRDDYLEWPEYFMAVAFLSAQRSKDP.SQVGACI.N.ENKIVGIGYNGMPNGCSDDLLPWRRT.
Retrocopy HSETTKKRDDYLEWPEYFMAVAFLSAQRSKDPHSQVGACIVNTENKIVGIGYNGMPNGCSDDLLPWRRTV

Parental  DSKLDTKYPYVCHAELNAIMNKNSADVKGCTMYVALFPCNECAKLIIQAGIKEVIYMSDKYHDSDETTAA
          DSKLDTKYPY.CHAELNAIMNKNSADVKGCTMYVALFPCNECAKLIIQAGIKEVIYMSDKYHDSDETTAA
Retrocopy DSKLDTKYPYMCHAELNAIMNKNSADVKGCTMYVALFPCNECAKLIIQAGIKEVIYMSDKYHDSDETTAA

Parental  RLMFDLAGIKFRKFTPKYSKIVIDFDSINSRPSQK
          RL.FDLAGIKFRKFT.KYSKIVIDFDSI.SRPSQK
Retrocopy RLTFDLAGIKFRKFTSKYSKIVIDFDSIDSRPSQK

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_124 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017516	3 retrocopies	retro_ecab_829, retro_ecab_830, retro_ecab_915,
Mus musculus	ENSMUSG00000031562	1 retrocopy	retro_mmus_3672,
Rattus norvegicus	ENSRNOG00000013215	1 retrocopy	retro_rnor_2937,
Sarcophilus harrisii	ENSSHAG00000015218	1 retrocopy	retro_shar_124 ,
Tursiops truncatus	ENSTTRG00000001460	1 retrocopy	retro_ttru_613,