RetrogeneDB ID: retro_shar_622

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856818.1:394766..395360(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000010366
• Aliases: None
• Description: None

Sequence

>retro_shar_622
TTGGCAGCTACAGGGGCATACCTGCACATATTTATACATTTTACTCCAACCAGCTTGCTCTTCCCCTTGGATTGCTTAGG
ACTGATCCCATGGCTTGTAGGAATGCCTTACCATTGTAAAACTGAAAAGAAGAGACTTCTTATTGTGTCTGGATTCACCT
TCGTTGTAGGAAGTGGTCTGGGCCCTACCCTGGATTTATGCATGACTGCTAATCCAAACATTGTTCCCATCTCCTAGGCT
GGAACTGCAATTGTCTTCAGCTGTTTTACCTTGAGTTCAGTTCTTGCAAGGCATCATGGCTATGTCTTCCTAGGGGGCAT
CTTGATTTCTGCCATGAGCCTTATTTTTGTCTCTTCTTTGGGGAACCTCTTATTTGGATTTCATTTGCTCTTTCAGGTGA
ATCTGTATTTGGGACTGGCAGTTATTTGTGGCTTTATCCTTTTTGATACTCAGCTCATAATAAAAAAAGTATGAGAATGG
AGATAAGGATATATCTGACACGGTGTTGACCTCTTCTTGGATTTTGCCGTCTTCTTATGGGGATTTTTGATGATCCTGGC
AATGAATGAAAAGAACAAGATGAAATAAAAGGAA

Alignment

ORF - retro_shar_622 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.5 %
• Parental protein coverage: 83.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAAAGAYVHVVTHFIQAGLLSALGSLGLMIWLMATPHSHETEQKRLGLLAGFAFLTGVGLGPALDLCIAI
          .AA.GAY.H...HF....LL..L..LGL..WL...P....TE.KRL....GF.F..G.GLGP.LDLC...
Retrocopy LAATGAYLHIFIHFTPTSLLFPLDCLGLIPWLVGMPYHCKTEKKRLLIVSGFTFVVGSGLGPTLDLCMTA

Parental  NPSIIPTSFLGTAMIFSCFTLSALYARRRSYLFLGGILMSAMSLMLFSSLGNLFFGSYWLFQANLYVGLV
          NP.I.P.S..GTA..FSCFTLS...AR...Y.FLGGIL.SAMSL...SSLGNL.FG...LFQ.NLY.GL.
Retrocopy NPNIVPIS*AGTAIVFSCFTLSSVLARHHGYVFLGGILISAMSLIFVSSLGNLLFGFHLLFQVNLYLGLA

Parental  VMCGFVLFDTQLIIEKA-ENGDKD-YIWHCVDLFLDFVTLFRKLMMILAMNEKDKKKEKK
          V.CGF.LFDTQLII.K..ENGDKD.YI.H.VDLFLDF........MILAMNEK.K.K.K.
Retrocopy VICGFILFDTQLIIKKV>ENGDKD<YI*HGVDLFLDFAVFLWGFLMILAMNEKNKMK*KE

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_622 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018588	1 retrocopy	retro_btau_762,
Canis familiaris	ENSCAFG00000008400	2 retrocopies	retro_cfam_1220, retro_cfam_876,
Callithrix jacchus	ENSCJAG00000021032	1 retrocopy	retro_cjac_272,
Dasypus novemcinctus	ENSDNOG00000007882	2 retrocopies	retro_dnov_164, retro_dnov_857,
Macropus eugenii	ENSMEUG00000015590	4 retrocopies	retro_meug_1076, retro_meug_1706, retro_meug_2157, retro_meug_48,
Monodelphis domestica	ENSMODG00000004277	2 retrocopies	retro_mdom_210, retro_mdom_250,
Otolemur garnettii	ENSOGAG00000005137	2 retrocopies	retro_ogar_1074, retro_ogar_3470,
Pteropus vampyrus	ENSPVAG00000016821	1 retrocopy	retro_pvam_755,
Sarcophilus harrisii	ENSSHAG00000010366	1 retrocopy	retro_shar_622 ,
Ictidomys tridecemlineatus	ENSSTOG00000001165	2 retrocopies	retro_itri_1273, retro_itri_564,
Tarsius syrichta	ENSTSYG00000002427	1 retrocopy	retro_tsyr_916,