RetrogeneDB ID: retro_shar_541

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849867.1:1604531..1605027(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000011593
• Aliases: None
• Description: None

Sequence

>retro_shar_541
CAGTTTGCTTCATTATATTACTATTGTCTGGCTCTCATGTATTGTTGGATGCTTCACATCAAAATGGACCATGCTATAAA
GTATTCAAAAGCATTAATTGACAATTTCAAAAATCCATTTTAAGCTGTCCAGGTCTCATCTCCATGGGGTGCCAGTGAAA
AGAGCACAGGAACTCCATCCCCCATGTTTCCCAGCCCTGTTCTTGTCAGCTCAATATGATCTCAGGGGAGTCTTCCAAGA
ACTAGCACCATCTTCCCCATCATCCATAATTAGCAATCCACATCAAATCCATCAGGCAGCAGCCAACCATATCAGCATCA
CTAACATTCTGCACAGCTATGACTACTGGGAGATGGCTGACAACCTTGCCAAAGAGAACAAAGAGTACTCTAATGATCTG
GATTTGCTGCTGGGGCTCCTCATCATGTATTGCAGTATGGATCACCTAGGTCAGTACTCCCAGCAAGGACTACATTGGCT
GTAAAATGATGTTCAC

Alignment

ORF - retro_shar_541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.66 %
• Parental protein coverage: 65.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QLAALCYRCLALLYWRMFRLKRDHAVKYSKALIDYFKNSSKAAQAPSPWSASGKSTGTPSPMSPSPSPVS
          Q.A.L.Y.CLAL.Y..M...K.DHA.KYSKALID.FKN...A.Q..SPW.AS.KSTGTPSPM.PSP..VS
Retrocopy QFASLYYYCLALMYCWMLHIKMDHAIKYSKALIDNFKNPF*AVQVSSPWGASEKSTGTPSPMFPSPVLVS

Parental  SVGSQGSLSSTST-PSPSSIISIPHRIHQMAANHVSITNSILHSYDYWEMADNLAKENREFFNDLDLLMG
          S..SQGSL..TST..SPSSIIS.PH.IHQ.AANH.SITN.ILHSYDYWEMADNLAKEN.E..NDLDLL.G
Retrocopy SI*SQGSLPRTST>SSPSSIISNPHQIHQAAANHISITN-ILHSYDYWEMADNLAKENKEYSNDLDLLLG

Parental  PVTLHSSMEHLVQYSQQGLHWLRNSVH
          ......SM.HL.QYSQQGLHWL.N.VH
Retrocopy LLIMYCSMDHLGQYSQQGLHWL*NDVH

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_541 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000011593	1 retrocopy	retro_shar_541 ,