RetrogeneDB ID: retro_shar_590

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850854.1:28015..28356(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM96B
• Ensembl ID: ENSSHAG00000004698
• Aliases: None
• Description: family with sequence similarity 96, member B [Source:HGNC Symbol;Acc:24261]

Sequence

>retro_shar_590
CTGATCCAGTCCATCAATGATCCTGAGCACCCACTCATCTTGGAAGAGCTGAAGGTGGTGGATCAAGTCTGAGTAAAAGT
TAATGACGAGAGTACTGTGGCTGTGGAATTTACTCCCACAATTCCTCATTGCAGGATGGCAACATTAATCAGCTTGTCCA
TCAAAATCAAGCTGATCTGCTCCTTGCCTAAAAGGTTTAAGATGGATATTCACATTACTCTTGGGACAGATGTCTCAGAA
CTCACTGTGAACAAACAGCTTGCTAACAAGGAGTGTCCTGCAGCAGCTTTGGAGAATTCCCATTTACTGGAAGTTATAAC
CGATGTCTGTCAGCTTGTTCC

Alignment

ORF - retro_shar_590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.31 %
• Parental protein coverage: 67.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LIRSINDPEHPLTLEELNVVEQVRVKVNDKESTVAVEFTPTIPHCSMATLIGLSIKVKLIRSLPERFKMD
          LI.SINDPEHPL.LEEL.VV.QV.VKVND.ESTVAVEFTPTIPHC.MATLI.LSIK.KLI.SLP.RFKMD
Retrocopy LIQSINDPEHPLILEELKVVDQV*VKVND-ESTVAVEFTPTIPHCRMATLISLSIKIKLICSLPKRFKMD

Parental  VHITPGTHASEHAVNKQLADKERVAAALENSHLLEVV-NQCLSARS
          .HIT.GT..SE..VNKQLA.KE..AAALENSHLLEV..N.CLSA.S
Retrocopy IHITLGTDVSELTVNKQLANKECPAAALENSHLLEVI<NRCLSACS

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_590 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017164	1 retrocopy	retro_amel_1340,
Bos taurus	ENSBTAG00000013931	1 retrocopy	retro_btau_609,
Canis familiaris	ENSCAFG00000020394	2 retrocopies	retro_cfam_479, retro_cfam_802,
Felis catus	ENSFCAG00000029216	2 retrocopies	retro_fcat_1464, retro_fcat_697,
Mustela putorius furo	ENSMPUG00000005303	2 retrocopies	retro_mputfur_1547, retro_mputfur_302,
Mus musculus	ENSMUSG00000031879	1 retrocopy	retro_mmus_2927,
Sarcophilus harrisii	ENSSHAG00000004698	1 retrocopy	retro_shar_590 ,
Tarsius syrichta	ENSTSYG00000005006	2 retrocopies	retro_tsyr_1305, retro_tsyr_149,