RetrogeneDB ID: retro_shar_52

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867603.1:899427..900660(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000011738
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000016264
• Aliases: None
• Description: None

Sequence

>retro_shar_52
ATGCCTAAAATGGGGAATAAACCCAAATGGCGTAGGGGGGAAACCAGAAAGATCCAGTCGGCACTGCTCAGAGCAGTCTT
CCTGGCGTCTAATCCTCAGTATTTGGAAAGGAAGAGGATAGATTGGGAGGCTAGGCAGAAAATTGTCCTGTGGAAGAAAC
CGCTTGTTACCTTACACTACTTTTTACTGGAAACCCTGATCAACCTGAAGGGGTGGATTGTCAACCTATGGCGGTGGCGA
AGATTCCTGGTTGCACCTATGCTTTTGCTGGTCGTATTTGGGGCTACCTATTACATCGAGGGAGCTCACCAAAAGTATGT
ACACTATCTGGAGAAAAAGACACTGTGGTGCTGTTACTGGATTGGCCTCGGGATTCTTTCTTCTGTGGGTCTTGGAACAG
GTCTTCATACTTTTATGCTCTATCTAGGCCCTCACATTGCTGCTGTTACCCTGGCTGCCTATGAATGTAACACTCTTAAT
TTCCCAGAGCCACCTTATCCCGAGAGGATTGTTTGTCCAGAAGGAGGTATTGAAGCAACTGTGTCATTGTGGGCCATCCT
TTCCAAGGTCAGATTTGAAGCCTTCATGTGGGGTGTCGGCACAGCCATTGGAGAACTGCCCCCTTATTTCATGGCAAGGG
CAGCCCGAATGTCAGGTCCTGATGCTGATGACGAAGAGTTTGAAGAGTTTGAAGAGATGTTGGAAGAGTATGATTCTCCT
CGAGGTACTACTTCCTGGGCTAAGCAAAGCGTACAGAATCTGGTGAAGAAGGTTGGGTTTTTCGGAATATTAGCCTGTGC
TTCAATTCCAAACCCTCTATTTGACCTGGCAGGGATAGCATGTGGACATTTCCTGGTTCCTTTTTGGACCTTCTTTGGTG
CCACTCTCATTGGAAAAGCCATAGTGAAGATGCACATCCAGGAACTCTTTGTTGTTATGACCTTCAGCAAACATATCGTG
GAACAAATGGTTACTCTCATTGGTTCTGTCCCCAAAGTAGGCCCCTCTCTGCAGAAACTGTTCCAAGATTACTTAGATTC
AGAGAAGGTGAAGCTTCATAGCAAAACTGAGACAAAGAATGTGCCAGGGAAAGAAAACTGGGTATACTGGTTTTTTGAGA
AGTTGGTGATTGTGATGGTATTATACTTCATACTATCCATCATCAATTCCATGGCACAAAGCTACACTAAACGAATGCAG
CAGCAAATAAACTCACAGGACAAAATGAATTAA

Alignment

ORF - retro_shar_52 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.38 %
• Parental protein coverage: 58.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKKRRDREERLNIVLWRQPLITLQYFFLEILINLKEWTVKLWHRRSMVVSFLLLLAVLTATYYIEGTHQQ
          E.KR.D.E.R..IVLW..PL.TL.YF.LE.LINLK.W.V.LW..R...V...LLL.V..ATYYIEG.HQ.
Retrocopy ERKRIDWEARQKIVLWKKPLVTLHYFLLETLINLKGWIVNLWRWRRFLVAPMLLLVVFGATYYIEGAHQK

Parental  YVKFMEKKILWCAYWVGLGILSSVGLGTGLHTFLLYLGPHIASVTLAAYECNSVNFPEPPYPDQIICPDE
          YV...EKK.LWC.YW.GLGILSSVGLGTGLHTF.LYLGPHIA.VTLAAYECN..NFPEPPYP..I.CP.E
Retrocopy YVHYLEKKTLWCCYWIGLGILSSVGLGTGLHTFMLYLGPHIAAVTLAAYECNTLNFPEPPYPERIVCP-E

Parental  EGIEGSISLWTIISKVRLEACMWGAGTAIGELPPYFMARAARLSGAEPDDEEYQEFEEMLEHADSAQDNI
          .GIE...SLW.I.SKVR.EA.MWG.GTAIGELPPYFMARAAR.SG...DDEE..EFEEMLE..DS.....
Retrocopy GGIEATVSLWAILSKVRFEAFMWGVGTAIGELPPYFMARAARMSGPDADDEEFEEFEEMLEEYDSPRGTT

Parental  TKLILSIEDMIQKSNFNKILRCRS
          .....S......K..F..IL.C.S
Retrocopy SWAKQSVQNLVKKVGFFGILACAS

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_52 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000014339	1 retrocopy	retro_mdom_2,
Mus musculus	ENSMUSG00000018171	1 retrocopy	retro_mmus_2640,
Nomascus leucogenys	ENSNLEG00000000724	1 retrocopy	retro_nleu_818,
Rattus norvegicus	ENSRNOG00000003967	1 retrocopy	retro_rnor_527,
Sarcophilus harrisii	ENSSHAG00000016264	1 retrocopy	retro_shar_52 ,
Drosophila melanogaster	FBgn0052675	1 retrocopy	retro_dmel_49,