RetrogeneDB ID: retro_shar_469

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849598.1:1484278..1484643(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT21
• Ensembl ID: ENSSHAG00000009651
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 21 [Source:HGNC Symbol;Acc:13870]

Sequence

>retro_shar_469
CCCAGGCTTTAACAAATAGGCTGGCTCCAGGCTGTGAGCAGTTTGGGAACAGACATATCCAGCAGATCAAGCTTCTCACC
CTGGAGCTTACAGTCAACCTGTACTCTCTTACAAATTAAGCATTTGTTACAAAAAAAGACTCTTTATGAAAAAGCTCAGT
TGTAGTTCACTTTCAATGGGTGAATGAGGAGTTTAATAAACTTGGAATAAAGATGATGGTAGAAGGTGTTCTGATTGTGC
ACAAACACTGCTTACCACCATTTACTGCTATAACAAGGCACAACTCTCTCCAGCAAATTACTGGTGGTGAACTGAATCAA
AGAGAAGATGAAGTGGAAGGATATAAATGTTTAATGATAGGTATT

Alignment

ORF - retro_shar_469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.61 %
• Parental protein coverage: 54.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PNRSQTGWPRGVN-QFGNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKI
          P...Q.GW...V..QFGN..IQQ.K.LTLE.T.NLY.LTN..F.TK.....K.SSV...FQ...EEF.K.
Retrocopy PRL*QIGWLQAVS<QFGNRHIQQIKLLTLELTVNLYSLTN*AFVTKKDSL*K-SSVVVHFQWVNEEFNKL

Parental  GMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEI
          G....VEGVLIVH.H.LP...............GGELN..EDEVEG.K.LM..I
Retrocopy GIKMMVEGVLIVHKHCLPPFTAITRHNSLQQITGGELNQREDEVEGYKCLMIGI

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_469 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 22 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016628	1 retrocopy	retro_amel_540,
Callithrix jacchus	ENSCJAG00000012724	3 retrocopies	retro_cjac_1121, retro_cjac_2211, retro_cjac_4100,
Cavia porcellus	ENSCPOG00000003705	1 retrocopy	retro_cpor_1054,
Equus caballus	ENSECAG00000001043	1 retrocopy	retro_ecab_292,
Erinaceus europaeus	ENSEEUG00000003402	1 retrocopy	retro_eeur_35,
Echinops telfairi	ENSETEG00000013634	1 retrocopy	retro_etel_622,
Felis catus	ENSFCAG00000008669	1 retrocopy	retro_fcat_1843,
Loxodonta africana	ENSLAFG00000028465	1 retrocopy	retro_lafr_610,
Myotis lucifugus	ENSMLUG00000004968	2 retrocopies	retro_mluc_1576, retro_mluc_999,
Macaca mulatta	ENSMMUG00000019906	1 retrocopy	retro_mmul_1360,
Mustela putorius furo	ENSMPUG00000003451	1 retrocopy	retro_mputfur_158,
Mus musculus	ENSMUSG00000031754	3 retrocopies	retro_mmus_1949, retro_mmus_1950, retro_mmus_2142,
Oryctolagus cuniculus	ENSOCUG00000017224	2 retrocopies	retro_ocun_154, retro_ocun_87,
Otolemur garnettii	ENSOGAG00000014888	2 retrocopies	retro_ogar_1450, retro_ogar_630,
Ochotona princeps	ENSOPRG00000006689	1 retrocopy	retro_opri_637,
Pteropus vampyrus	ENSPVAG00000014583	2 retrocopies	retro_pvam_533, retro_pvam_711,
Sarcophilus harrisii	ENSSHAG00000009651	1 retrocopy	retro_shar_469 ,
Sus scrofa	ENSSSCG00000029848	2 retrocopies	retro_sscr_117, retro_sscr_185,
Tupaia belangeri	ENSTBEG00000007664	1 retrocopy	retro_tbel_4003,
Tarsius syrichta	ENSTSYG00000014602	4 retrocopies	retro_tsyr_1685, retro_tsyr_1888, retro_tsyr_790, retro_tsyr_988,
Tursiops truncatus	ENSTTRG00000013545	1 retrocopy	retro_ttru_1087,
Vicugna pacos	ENSVPAG00000003701	2 retrocopies	retro_vpac_340, retro_vpac_605,