RetrogeneDB ID: retro_shar_454

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849545.1:1424096..1424403(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000001787
• Aliases: None
• Description: None

Sequence

>retro_shar_454
ATTAACAAAATGAACAAAGATGCACAGATGAGAGCAACTATTAACAAGAAACTGATAGAAACTGGTGAACAAGAACGACT
TAAAGAATTGCTAAGAGCTAAATTAATCAAATGTGGTTGGAAAGATCAATTAAAAGCTCATTGTAAAAATGTGATTAAAG
AAAAAGGATTAGAACATATAACATGTTCTAATTTTGATGACTTGGTAGCAGAGATAACCCCGAAAGGCAGAGCACTTGTA
CCCCGACTGTGTGAAGAAGGAACTTTTTCAAAGAATAAGAACTTTCCTTGCTCAGTATGCCAGCCTT

Alignment

ORF - retro_shar_454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  INKMNKDAQMRATINQKLIETGERERLKELLRAKLIECGWKDQLKAHCKDVIKEKGLEHVT---VDDLVA
          INKMNKDAQMRATIN.KLIETGE.ERLKELLRAKLI.CGWKDQLKAHCK.VIKEKGLEH.T....DDLVA
Retrocopy INKMNKDAQMRATINKKLIETGEQERLKELLRAKLIKCGWKDQLKAHCKNVIKEKGLEHITCSNFDDLVA

Parental  EITPKGRALV-PDSVKKELLQRIRTFLAQHASL
          EITPKGRALV.PD.VKKEL.QRIRTFLAQ.ASL
Retrocopy EITPKGRALV>PDCVKKELFQRIRTFLAQYASL

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_454 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 21 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003039	1 retrocopy	retro_acar_1,
Bos taurus	ENSBTAG00000007387	1 retrocopy	retro_btau_754,
Callithrix jacchus	ENSCJAG00000006389	4 retrocopies	retro_cjac_1206, retro_cjac_1355, retro_cjac_1436, retro_cjac_550,
Cavia porcellus	ENSCPOG00000010988	1 retrocopy	retro_cpor_927,
Dasypus novemcinctus	ENSDNOG00000007377	1 retrocopy	retro_dnov_25,
Equus caballus	ENSECAG00000023565	1 retrocopy	retro_ecab_715,
Erinaceus europaeus	ENSEEUG00000012383	3 retrocopies	retro_eeur_125, retro_eeur_220, retro_eeur_512,
Echinops telfairi	ENSETEG00000010882	2 retrocopies	retro_etel_1826, retro_etel_450,
Microcebus murinus	ENSMICG00000012948	3 retrocopies	retro_mmur_1041, retro_mmur_773, retro_mmur_793,
Myotis lucifugus	ENSMLUG00000027585	1 retrocopy	retro_mluc_357,
Macaca mulatta	ENSMMUG00000006104	2 retrocopies	retro_mmul_1094, retro_mmul_1490,
Mustela putorius furo	ENSMPUG00000005873	2 retrocopies	retro_mputfur_1128, retro_mputfur_323,
Mus musculus	ENSMUSG00000022338	3 retrocopies	retro_mmus_1055, retro_mmus_1795, retro_mmus_3511,
Nomascus leucogenys	ENSNLEG00000004284	3 retrocopies	retro_nleu_2535, retro_nleu_2584, retro_nleu_2585,
Pongo abelii	ENSPPYG00000025888	1 retrocopy	retro_pabe_750,
Rattus norvegicus	ENSRNOG00000004681	1 retrocopy	retro_rnor_2193,
Sorex araneus	ENSSARG00000009845	1 retrocopy	retro_sara_561,
Sarcophilus harrisii	ENSSHAG00000001787	4 retrocopies	retro_shar_454 , retro_shar_675, retro_shar_815, retro_shar_816,
Tupaia belangeri	ENSTBEG00000000273	4 retrocopies	retro_tbel_2257, retro_tbel_324, retro_tbel_4307, retro_tbel_823,
Tarsius syrichta	ENSTSYG00000005590	1 retrocopy	retro_tsyr_673,
Tursiops truncatus	ENSTTRG00000001742	3 retrocopies	retro_ttru_46, retro_ttru_845, retro_ttru_997,