RetrogeneDB ID: retro_shar_820

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867584.1:2827145..2828058(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000017109
• Aliases: None
• Description: None

Sequence

>retro_shar_820
ATGGAGAATGAACAGCCAGAAGCAACCTTCTCTAGTACTGAAACTAGGGTGGATTGGTTAAGTGCTCTGCCAAATATATG
GAAGGAAAGCAGGCCCTTAAAAGATCTAGAAACACTGATGAGATGGTGGAAGTGCACATTTTGTTAAGAGTAAAAATGCT
GGAACAGTGCTTAGGAAAGGAGGCGAAAATATTAAAACGTTTTATACAGACTACTACTGCCAGTGTTTCAATCCTAGACA
GCAGTTGCCCTGAGCACGTGTTGAGTATCAGTGCAGATATCAAAACAAATGGGGAAATTTGGAAGAAAATCATTCCCAGG
TAGGAAAAGGGCCTTTAGTTGCCATCCCCTACTGCAACCAGCCAGCTCCTACTGGGATCTGATGCTAGGGAATGCTTAAG
TTACCAACACTTTAAAGGAAGCAACTTTGACTGCAAGTGAAGACTGTTGATTCACCACAGATGGCAAGAAGAATTATTGG
GGTCAAAGGTGCCAAAATCAAAGAACTTTGAAAAAACACTCAGACAACTAGCAAGCTTTTCCGGGAATGCTGCTGTCTTC
ATTCTACTAAGAGAGTTGTTATTAGCGGTGGAAAGCTTGATAGGGTTGTGGAGTACAGAAAGACCACATTGGATCTTATA
TATGAGTCTCCTGTCAAAGGATGTGCACAACCCTGTGATCCCAGTTTCCATGATGAAACATATGACTGTGGTGGGTTCAC
AATGAAATGTGATGATAGATAAGGATGCTCTGTAGGATTTCCCTTGTGAGGCAAAGAAGGCAGCGTTCATAGAATGCCTT
CAGCTCCTGATGGGTGTCCTATGCCCCAATCTAGAAGACATTATGATGAAGTGAGCCCTTGCAGAGAACCCCTGCCACTT
CCTCCTTGATGTGGTGGTAAAGTGGCAGAGAGA

Alignment

ORF - retro_shar_820 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.37 %
• Parental protein coverage: 73.54 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  METEQPEETFPNTETN-GEFGKRPAEDMEEEQAFKRSRNTDEMVELRILL-QSKNAGAVIGKGGKNIKAL
          ME.EQPE.TF..TET..G...K..A..ME..QA.KRSRNTDEMVE..ILL..SKNAG.V..KGG.NIK..
Retrocopy MENEQPEATFSSTETR<GGLVKCSAKYMEGKQALKRSRNTDEMVEVHILL<KSKNAGTVLRKGGENIKTF

Parental  RTDY-NASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQH
          .TDY..ASVS..DSS.PE..LSISADI.T.GEI.KKIIP..E.GL.LPSPTATSQL.L.SDA.ECL.YQH
Retrocopy YTDY>TASVSILDSSCPEHVLSISADIKTNGEIWKKIIPR*EKGL*LPSPTATSQLLLGSDARECLSYQH

Parental  YKGSDFDCELRLLIHQ-SLAGGIIGVKGAKIKELRENTQTTIKLFQE-CCPHSTDRVVLIGGKPDRVVEC
          .KGS.FDC..RLLIH....A..IIGVKGAKIKEL..NTQTT.KLF.E.CC.HST.RVV..GGK.DRVVE.
Retrocopy FKGSNFDCK*RLLIHH<QMARRIIGVKGAKIKEL*KNTQTTSKLFRECCCLHSTKRVVISGGKLDRVVEY

Parental  IKIILDLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGR-GGFDRMPPGRGGRPMP
          .K..LDLI.ESP.KG.AQP.DP.F.DETYD.GGFTM..DDR.G..VGFP..G..G...RMP....G.PMP
Retrocopy RKTTLDLIYESPVKGCAQPCDPSFHDETYDCGGFTMKCDDR*GCSVGFPL*GKEGSVHRMPSAPDGCPMP

Parental  PSRRDYDDMSPRRGPPPPPPGRGGRGGSR
          .SRR.YD..SP.R.P.P.PP..GG....R
Retrocopy QSRRHYDEVSPCREPLPLPP*CGGKVAER

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_820 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 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021131	2 retrocopies	retro_btau_468, retro_btau_605,
Choloepus hoffmanni	ENSCHOG00000010832	2 retrocopies	retro_chof_1023, retro_chof_1589,
Dasypus novemcinctus	ENSDNOG00000000026	4 retrocopies	retro_dnov_1433, retro_dnov_1820, retro_dnov_2316, retro_dnov_2638,
Dipodomys ordii	ENSDORG00000016024	1 retrocopy	retro_dord_673,
Homo sapiens	ENSG00000165119	3 retrocopies	retro_hsap_2323, retro_hsap_2674, retro_hsap_3385,
Gorilla gorilla	ENSGGOG00000015500	2 retrocopies	retro_ggor_1764, retro_ggor_1866,
Loxodonta africana	ENSLAFG00000026567	1 retrocopy	retro_lafr_809,
Macropus eugenii	ENSMEUG00000006975	3 retrocopies	retro_meug_271, retro_meug_357, retro_meug_484,
Microcebus murinus	ENSMICG00000015780	3 retrocopies	retro_mmur_1562, retro_mmur_235, retro_mmur_448,
Myotis lucifugus	ENSMLUG00000005871	2 retrocopies	retro_mluc_128, retro_mluc_561,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666,
Mus musculus	ENSMUSG00000021546	2 retrocopies	retro_mmus_1131, retro_mmus_2137,
Nomascus leucogenys	ENSNLEG00000003486	3 retrocopies	retro_nleu_1178, retro_nleu_1815, retro_nleu_973,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820 ,
Sus scrofa	ENSSSCG00000022760	1 retrocopy	retro_sscr_437,
Tupaia belangeri	ENSTBEG00000001289	1 retrocopy	retro_tbel_2491,
Tarsius syrichta	ENSTSYG00000001196	3 retrocopies	retro_tsyr_1664, retro_tsyr_1796, retro_tsyr_2149,
Tursiops truncatus	ENSTTRG00000004906	1 retrocopy	retro_ttru_1622,
Tursiops truncatus	ENSTTRG00000016693	7 retrocopies	retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,