RetrogeneDB ID: retro_shar_537

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849854.1:470594..470973(+)
• Located in intron of: ENSSHAG00000006876

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS7B
• Ensembl ID: ENSSHAG00000009961
• Aliases: None
• Description: COP9 signalosome subunit 7B [Source:HGNC Symbol;Acc:16760]

Sequence

>retro_shar_537
AAACTTATAAAAAGTGTTAATGCTATTTATTATCAGTTGCTGTCTGCCTATAGAACATACCCAGATCATATAGTCACCAA
GGACACCCTATCTAAACTAAGCATGGGTTCCTAAGAACAAGCTAAATCATCTCACTATTGTAAGCTTGGCCGCAAGAATG
AAGTGTATTCTTTGCCCAGTGCCTCTGAAGAATCTCAAGATGCAGAACCTTTGGCAGCTAGAAGATCTCACCAATGAAAC
TGTCTATGTGGGCACCATTCAAAGCAAATTGGATCAGTACAACTAGCTACTTGAAGTGGACTTTTGCATTGGCCAAGACA
TTCAAGGGAAGGACATGGACAATCTTATCAAAACCTTGCAAGAATGGTGTGACAAATGT

Alignment

ORF - retro_shar_537 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.79 %
• Parental protein coverage: 60.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QLAEGANAAYFQLLSLFAYGTYPDYLANKDSLPELTPAQ-KNKLKHLTIVSLAARMKCIPYSVLLKDLEM
          .L....NA.Y.QLLS..AY.TYPD....KD.L..L.....KNKL.HLTIVSLAARMKCI...V.LK.L.M
Retrocopy KLIKSVNAIYYQLLS--AYRTYPDHIVTKDTLSKLSMGS>KNKLNHLTIVSLAARMKCILCPVPLKNLKM

Parental  RNLRELEDLIIEAVYTDIIQGKLDQRNQLLEVDFCIGRDIQKKDINTLVKTLQEWCDGC
          .NL..LEDL..E.VY...IQ.KLDQ.N.LLEVDFCIG.DIQ.KD...L.KTLQEWCD.C
Retrocopy QNLWQLEDLTNETVYVGTIQSKLDQYN*LLEVDFCIGQDIQGKDMDNLIKTLQEWCDKC

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_537 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013630	1 retrocopy	retro_cjac_3894,
Oryctolagus cuniculus	ENSOCUG00000016918	1 retrocopy	retro_ocun_1194,
Ochotona princeps	ENSOPRG00000008376	1 retrocopy	retro_opri_850,
Sarcophilus harrisii	ENSSHAG00000009961	1 retrocopy	retro_shar_537 ,