RetrogeneDB ID: retro_shar_786

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL864819.1:1979086..1979362(-)
• Located in intron of: ENSSHAG00000015402

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000004796
• Aliases: None
• Description: None

Sequence

>retro_shar_786
GTGGTAGTGCAGGATTGGGGTCCCTGGGGAGGAGCAGACATATCGCATAAAGAATTTTACTATTCGGACAAATATGATGA
TGAGGAGTTTGAGTACTGATACATCACGTTGCCCAAGGACATAGTCATACTGGTCCCTAAGACCAATTTGCTGTCTGAGT
CTGAGTGGAAGAACCTTGGTGTCCAGCAGAGTCAGGGATGGGTCCATTACATGATCCATGAACCAGAGCCTCACTTCTTG
CTGTTCCAGCAGCCACTGCCCAAGAAGCCTAAGAAG

Alignment

ORF - retro_shar_786 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVARGWGPRGGADMSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMTESEWRNLGVQQSQGWVHY
          .V...WGP.GGAD.SHK..YYSDKYDDEEFEY....LPKDI..LVPKT.L..ESEW.NLGVQQSQGWVHY
Retrocopy VVVQDWGPWGGADISHKEFYYSDKYDDEEFEY*YITLPKDIVILVPKTNLLSESEWKNLGVQQSQGWVHY

Parental  MIHEPEPHILLFRRPLPKKPKK
          MIHEPEPH.LLF..PLPKKPKK
Retrocopy MIHEPEPHFLLFQQPLPKKPKK

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_786 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 10 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000033635	10 retrocopies	retro_cjac_13, retro_cjac_1441, retro_cjac_1478, retro_cjac_1779, retro_cjac_2040, retro_cjac_2212, retro_cjac_2649, retro_cjac_276, retro_cjac_57, retro_cjac_876,
Cavia porcellus	ENSCPOG00000024061	2 retrocopies	retro_cpor_859, retro_cpor_941,
Dipodomys ordii	ENSDORG00000003764	6 retrocopies	retro_dord_25, retro_dord_290, retro_dord_599, retro_dord_64, retro_dord_647, retro_dord_739,
Erinaceus europaeus	ENSEEUG00000015895	1 retrocopy	retro_eeur_302,
Homo sapiens	ENSG00000173207	1 retrocopy	retro_hsap_27,
Gorilla gorilla	ENSGGOG00000013419	4 retrocopies	retro_ggor_10, retro_ggor_1070, retro_ggor_2739, retro_ggor_659,
Myotis lucifugus	ENSMLUG00000002408	1 retrocopy	retro_mluc_1303,
Otolemur garnettii	ENSOGAG00000006384	10 retrocopies	retro_ogar_1673, retro_ogar_1703, retro_ogar_1713, retro_ogar_1983, retro_ogar_2317, retro_ogar_245, retro_ogar_3310, retro_ogar_450, retro_ogar_530, retro_ogar_877,
Rattus norvegicus	ENSRNOG00000042561	1 retrocopy	retro_rnor_97,
Sarcophilus harrisii	ENSSHAG00000004796	1 retrocopy	retro_shar_786 ,