RetrogeneDB ID: retro_shar_184

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834580.1:29064..29347(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HN1L
• Ensembl ID: ENSSHAG00000012700
• Aliases: None
• Description: hematological and neurological expressed 1-like [Source:HGNC Symbol;Acc:14137]

Sequence

>retro_shar_184
ATATTTAGGTCTCCAGTCACCATTACCATATCATTAGTATATCCAAATAAGCCCAAAGATCATATTGTCTTATGTGAAGG
TGAGGACACAAAATTGCAACTCAGAGCTAAAGAGAATATATAATCATCTTAAGAACATGATGAGAAATGTGACCAAAAAA
AAGGAGGATCGAGTCAAGGAAACTGAGGCTAAACCCAAGCCTAACAAGCACAGCCCAAATTGGGCACACTCATACAACAA
AGTCCTCAATCCACCAGGTGACAAATTCAGCATCTCTTTCTAC

Alignment

ORF - retro_shar_184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.66 %
• Parental protein coverage: 54.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IFGSPVTLTAPLAHPNKPKDHIVLCEGEDTKLQLRATENTQSSREEHDEKCD-KGKEERAKETESNLKID
          IF.SPVT.T..L..PNKPKDHIVLCEGEDTKLQLRA.EN..SS..EHDEKCD....E.R.KETE...K..
Retrocopy IFRSPVTITISLVYPNKPKDHIVLCEGEDTKLQLRAKENI*SS-*EHDEKCD>XXXEDRVKETEAKPKPN

Parental  NHEPRLGPRPRSHNKVLNPPGGKSSISFY
          .H.P.......S.NKVLNPPG.K.SISFY
Retrocopy KHSPNWA---HSYNKVLNPPGDKFSISFY

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_184 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008232	1 retrocopy	retro_amel_1019,
Cavia porcellus	ENSCPOG00000005352	2 retrocopies	retro_cpor_749, retro_cpor_892,
Dipodomys ordii	ENSDORG00000007521	1 retrocopy	retro_dord_269,
Macropus eugenii	ENSMEUG00000008873	4 retrocopies	retro_meug_1471, retro_meug_1628, retro_meug_189, retro_meug_258,
Mus musculus	ENSMUSG00000024165	3 retrocopies	retro_mmus_1204, retro_mmus_655, retro_mmus_709,
Oryctolagus cuniculus	ENSOCUG00000015551	1 retrocopy	retro_ocun_275,
Pteropus vampyrus	ENSPVAG00000016673	1 retrocopy	retro_pvam_99,
Rattus norvegicus	ENSRNOG00000024661	2 retrocopies	retro_rnor_25, retro_rnor_560,
Sorex araneus	ENSSARG00000012440	1 retrocopy	retro_sara_335,
Sarcophilus harrisii	ENSSHAG00000012700	1 retrocopy	retro_shar_184 ,
Tursiops truncatus	ENSTTRG00000011377	1 retrocopy	retro_ttru_429,