RetrogeneDB ID: retro_shar_830

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867623.1:1074058..1074689(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000015128
• Aliases: None
• Description: None

Sequence

>retro_shar_830
AAAAGTTTTCTTGCCCCACTTGGCTTGAATATGATATTGATGGAAAATACTTGTGATATGACTATTGATAATGGTGGTTA
CAAGCATCCTGAATTCATTAGAGGTAGAACATCCAGCAGCTGATACTCTTTGTGAACTGGTTGATCCACAAGATAGGGAA
GTTAGAGCCCGTAGGATATCTGTGGCTATTATCGCAGTCAGGACATCAAAGAAATGCTGACGAGTCAAGTCAGCAATTCA
CCCCACATCAATCATCGGTGCCCATTGACTGGTCTGGAAGGAAGTAGTGTACTTTATTGATCAGAACTTCATCATTAGCA
CAGGTGAACTTGGCAAAGATTATAGAAGTAAGGCTGCTAAAACATCCATATCTTCTAAGGCCATTGGAATTGATGGCAAT
TCCTTTGCCAATATGGTAATAGAGGAAGTACTTACAGCAAAAGATACAGAGGTGAAAGGTCAGCTTTGATTTCTACTCAA
CTCTGTTATTGCTTTGAAGTCCTGTGGCAAAAGTCAGAAGGAAAGTATGCGTATAAATGGTTATGGACCTAATTGTATGG
TGGAATCATGGGGTGGGCCCAAGAAAATAATGAATGCAAAAACCCTTTGCCTTGACTTCAACCTACCAAAA

Alignment

ORF - retro_shar_830 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.6 %
• Parental protein coverage: 84.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KSSLGPVGLDKMLVDDIGDVTITNDG-ATILKLLEVEHPAAKVLCELADLQDKEVGDGTTSVVIIAAELL
          KS.L.P.GL...L.....D.TI.N.G...IL..LEVEHPAA..LCEL.D.QD.EV.....SV.IIA....
Retrocopy KSFLAPLGLNMILMENTCDMTIDNGG>TSILNSLEVEHPAADTLCELVDPQDREVRARRISVAIIAVRTS

Parental  KNADELVKQKIHPTSIIGGYRLACKEAVRYINENLIINTDELGKDCLINAAKTSMSSKIIGIDGDFFANM
          K.....VK..IHPTSIIG...L..KE.V..I..N.II.T.ELGKD....AAKTS.SSK.IGIDG..FANM
Retrocopy KKC*R-VKSAIHPTSIIGAH*LVWKEVVYFIDQNFIISTGELGKDYRSKAAKTSISSKAIGIDGNSFANM

Parental  VVDAVLAVKYTDVKGQPRFPVNSINVLKAHGRSQKESMLINGYALNCVVASQGMPKRIVNAKIACLDFSL
          V...VL..K.T.VKGQ..F..NS...LK..G.SQKESM.INGY..NC.V.S.G.PK.I.NAK..CLDF.L
Retrocopy VIEEVLTAKDTEVKGQL*FLLNSVIALKSCGKSQKESMRINGYGPNCMVESWGGPKKIMNAKTLCLDFNL

Parental  QK
          .K
Retrocopy PK

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_830 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.

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015405	1 retrocopy	retro_amel_828,
Callithrix jacchus	ENSCJAG00000011792	2 retrocopies	retro_cjac_1867, retro_cjac_2193,
Equus caballus	ENSECAG00000017953	1 retrocopy	retro_ecab_798,
Homo sapiens	ENSG00000120438	1 retrocopy	retro_hsap_3722,
Gorilla gorilla	ENSGGOG00000014063	1 retrocopy	retro_ggor_2514,
Microcebus murinus	ENSMICG00000007998	1 retrocopy	retro_mmur_795,
Macaca mulatta	ENSMMUG00000012846	1 retrocopy	retro_mmul_1696,
Oryctolagus cuniculus	ENSOCUG00000013847	1 retrocopy	retro_ocun_1577,
Pongo abelii	ENSPPYG00000017146	1 retrocopy	retro_pabe_3135,
Pan troglodytes	ENSPTRG00000018760	1 retrocopy	retro_ptro_2617,
Pteropus vampyrus	ENSPVAG00000005316	1 retrocopy	retro_pvam_522,
Rattus norvegicus	ENSRNOG00000014160	1 retrocopy	retro_rnor_2091,
Sorex araneus	ENSSARG00000002463	1 retrocopy	retro_sara_624,
Sarcophilus harrisii	ENSSHAG00000015128	1 retrocopy	retro_shar_830 ,
Ictidomys tridecemlineatus	ENSSTOG00000005572	1 retrocopy	retro_itri_1274,