RetrogeneDB ID: retro_shar_710

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861570.1:349012..349725(-)
• Located in intron of: ENSSHAG00000006717

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK1D
• Ensembl ID: ENSSHAG00000007638
• Aliases: None
• Description: casein kinase 1, delta [Source:HGNC Symbol;Acc:2452]

Sequence

>retro_shar_710
AGGAACTGCTCATTATGCCCCCATCAACACTCATCTTGGAATTGAAGGGATGACTTGGAGTCCCTGGGCTATGTGTTGAT
GTACTTCAATTTGGGTTCCCTTCCCTGGCAGGGGCTGAAGGCTGCTACCAAGAGACAAAAATACGAAAGAATTAGTGAAA
AGAAAATGTCCACTCCCATTGAAGTATTATGTAAAGGCTACCCTTCTGAATTTGCCACATTCCTGAATTTCTATCGTTCG
TTGCGTTTTGATGACAAACCTGACAATTCCTACCTGAGACAGTTCTTCTTCAGGAACCTGTTCCATCGCCAGGGTTTTTC
ATATGACTATGTGTTTGACTGGAACATGTTAAAATTTGGTGCCAGCCGGGCAGCTGATGATGCCGAAAGGGAACACCGGG
ATTGAGAGGAACGATTGAGACACTACCAAAATCCAACTACTTGGGGTCTCCCTTCCACTGCATCAGACCGCCTGAGGGAA
ACACAAGATGTAGCTCCTCCCACTCCCCTCATCCCTACCTCACATACTGCTAACACCTCTCCTCGGCCTGTCTCTGGAAT
GGAAAGAGAGCGGAAAGTGAGTATGAGACTGCATTGTGGTGCCCCAGTCAATATCTCTTCATCTGATTTAACAGGCCGAC
AAGATACCTCTCGCATGTCAACCTCACAGATTCCGATGGGGTGATTTCCAGTGGTCTTCAGTCTGTTGTGCAC

Alignment

ORF - retro_shar_710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.45 %
• Parental protein coverage: 60.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSE
          R..S...H.......RDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSE
Retrocopy RNCSLCPHQHSSWN*RDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSE

Parental  FATYLNFCRSLRFDDKPDYSYLRQL-FRNLFHRQGFSYDYVFDWNMLKFGASRAADDAERERRDREERLR
          FAT.LNF.RSLRFDDKPD.SYLRQ..FRNLFHRQGFSYDYVFDWNMLKFGASRAADDAERE.RD.EERLR
Retrocopy FATFLNFYRSLRFDDKPDNSYLRQFFFRNLFHRQGFSYDYVFDWNMLKFGASRAADDAEREHRD*EERLR

Parental  HSRNPTTRGLPSTASGRLRGTQDVAPPTPLTPTSHTANTSPRPVSGMERERKVSMRLHRGAPVNISSSDL
          H..NPTT.GLPSTAS.RLR.TQDVAPPTPL.PTSHTANTSPRPVSGMERERKVSMRLH.GAPVNISSSDL
Retrocopy HYQNPTTWGLPSTASDRLRETQDVAPPTPLIPTSHTANTSPRPVSGMERERKVSMRLHCGAPVNISSSDL

Parental  TGRQDTSRMSTSQIP-GRVTSSGLQSVVH
          TGRQDTSRMSTSQIP...V.SSGLQSVVH
Retrocopy TGRQDTSRMSTSQIP<DGVISSGLQSVVH

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_710 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000008792	1 retrocopy	retro_meug_543,
Otolemur garnettii	ENSOGAG00000014866	1 retrocopy	retro_ogar_264,
Sorex araneus	ENSSARG00000005475	1 retrocopy	retro_sara_33,
Sarcophilus harrisii	ENSSHAG00000007638	2 retrocopies	retro_shar_260, retro_shar_710 ,
Sarcophilus harrisii	ENSSHAG00000015356	1 retrocopy	retro_shar_834,