RetrogeneDB ID: retro_meug_543

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold134229:1981..2708(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK1D
• Ensembl ID: ENSMEUG00000008792
• Aliases: None
• Description: casein kinase 1, delta [Source:HGNC Symbol;Acc:2452]

Sequence

>retro_meug_543
ATGGAGCTGAGAGTTGGGAATAGGTAACCGCTGGGTGGAAAGATTGGCAGTAGCTCCTTTGGAGGCATCTATCTTGGTAC
TGATATTTCTGCAGAAAAACTTGCCATCAAGCTCGAATATGTCAAAAACCAAACACCCTCAGCTCCATATTGAGAAAAAA
ATCTACAAAATGATGCAGGGAGGAGTGGGCATTCCTAAAATTAAATGGTGTGAGGCAGAAGAAGAGTATAATGTCATGGT
GATGGAGCTTTTGGGACCAAGCTTTGAAGTTGTCTTCAATTGCTGCTCAAGAAAATTCAGTGTGAAATTGTCCTTGTACT
TGCTGACCAGATGATTACTCAGATTGAATACATTCATTCAAACAACTTCATCCACCATGATGTGAAGCCGGATAATTTTC
CTATGGGACTGGAAAAAATGGGTAACCTGGCCTATACCATATACTTTGGGTTGGCCAAGAAGTACTGAGATGCTAGGACC
CATCAGCACATACCGATTGCGAGAATAAAAACCTCATAGGAACTGTTCTTTATGCCTCCATCAATGCTCATCTTGGAATT
GAACAGTCTCGAAGGGATGACTTGGAGTCCCTGGAATATGTGTTAATGTACTTCAATTTGGGCTCCCTGTCCTGGCGGGG
CTGAAGGCTGCTATCAAGAGACAAAAATACGAAAGAATTAGTGCAAAGAAAATGTCCACTCCCATTGAAGTGTTACGTAA
AGGCTAC

Alignment

ORF - retro_meug_543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.24 %
• Parental protein coverage: 59.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVK-TKHPQLHIESKIYKMMQGGVGIPTIK
          MELRVGNR..LG.KIGS.SFG.IYLGTDI.A.E..AIKLE.VK.TKHPQLHIE.KIYKMMQGGVGIP.IK
Retrocopy MELRVGNR*PLGGKIGSSSFGGIYLGTDISA-EKLAIKLEYVK>TKHPQLHIEKKIYKMMQGGVGIPKIK

Parental  WCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLK-TVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGL
          WC.AE..YNVMVMELLGPS.E..FN.CSRKFS.K..VL.LADQMI..IEYIHS.NFIH.DVKPDNF.MGL
Retrocopy WCEAEEEYNVMVMELLGPSFEVVFNCCSRKFSVK<IVLVLADQMITQIEYIHSNNFIHHDVKPDNFPMGL

Parental  GKKGNLVYIIDFGLAKKYRDARTHQHIPYR-ENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFN
          .K.GNL.Y.I.FGLAKKY.DARTHQHIP...ENKNL.GT..YASIN.HLGIEQSRRDDLESL.YVLMYFN
Retrocopy EKMGNLAYTIYFGLAKKY*DARTHQHIPIA<ENKNLIGTVLYASINAHLGIEQSRRDDLESLEYVLMYFN

Parental  LGSLPWQ-GLKAATKRQKYERISEKKMSTPIEVLCKGY
          LGSL.W..GLKAA.KRQKYERIS.KKMSTPIEVL.KGY
Retrocopy LGSLSWR<GLKAAIKRQKYERISAKKMSTPIEVLRKGY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_543 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_543 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 ,
Macropus eugenii	ENSMEUG00000012543	1 retrocopy	retro_meug_186,
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,