RetrogeneDB ID: retro_shar_579

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850441.1:161471..161798(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKIRIN2
• Ensembl ID: ENSSHAG00000011555
• Aliases: None
• Description: akirin 2 [Source:HGNC Symbol;Acc:21407]

Sequence

>retro_shar_579
AGAAGACATTAAGGATCTTGTTCCTGACAGTTAATTCCTTGCTATTATTCTGATTCACAGTCAGATGCATTTCTCCTTGG
TATATTAGCATTTACAGGTACCTCACCTGAAGAAGAACCACTATTTTAAAAAGAACAATTCTTCTTTACTCAAAAACAGA
CTGGAATGATCTGTGAATGTTTGTTGAAAGAATGGGAAAAGATGATTCATGAAGGGTATGAAAAAATATTGAACAAAAAA
CTTGCAGAACAACATAATGCATTTGTGAAATTTATGAATGATAAGATAACATGTTGATATAGAGAACAGCCTCCTAGTTT
TATTTCA

Alignment

ORF - retro_shar_579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.38 %
• Parental protein coverage: 97.32 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRHLETSFQQTDACCSSDSQPHAFLLNGPASPGTSSAASSPLKKEQPLFTLRQVGMICERLLKEREEKVR
          RRH......Q...C..SDSQ..AFLL...A..GTS........KEQ..FT..Q.GMICE.LLKE.E....
Retrocopy RRH*GSCS*QLIPCYYSDSQSDAFLLGILAFTGTSPEEEPLF*KEQFFFTQKQTGMICECLLKEWEKMIH

Parental  EEYEEILTTKLAEQYDAFVKFTHDQIMRRYGEQPASYVS
          E.YE.IL..KLAEQ..AFVKF..D.I...Y.EQP.S..S
Retrocopy EGYEKILNKKLAEQHNAFVKFMNDKITC*YREQPPSFIS

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_579 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 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003082	1 retrocopy	retro_cfam_1014,
Choloepus hoffmanni	ENSCHOG00000012160	1 retrocopy	retro_chof_413,
Callithrix jacchus	ENSCJAG00000000769	1 retrocopy	retro_cjac_2231,
Dasypus novemcinctus	ENSDNOG00000000549	1 retrocopy	retro_dnov_1788,
Homo sapiens	ENSG00000135334	1 retrocopy	retro_hsap_2991,
Gorilla gorilla	ENSGGOG00000002448	1 retrocopy	retro_ggor_2071,
Macaca mulatta	ENSMMUG00000002824	1 retrocopy	retro_mmul_1914,
Pongo abelii	ENSPPYG00000016831	1 retrocopy	retro_pabe_2477,
Pan troglodytes	ENSPTRG00000018409	1 retrocopy	retro_ptro_2023,
Rattus norvegicus	ENSRNOG00000008288	1 retrocopy	retro_rnor_1499,
Sorex araneus	ENSSARG00000006084	1 retrocopy	retro_sara_701,
Sarcophilus harrisii	ENSSHAG00000011555	2 retrocopies	retro_shar_363, retro_shar_579 ,
Sarcophilus harrisii	ENSSHAG00000017458	1 retrocopy	retro_shar_577,
Sus scrofa	ENSSSCG00000004307	1 retrocopy	retro_sscr_897,