RetrogeneDB ID: retro_meug_1896

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold7010:22916..23799(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSP90AB1
• Ensembl ID: ENSMEUG00000013735
• Aliases: None
• Description: heat shock protein 90kDa alpha (cytosolic), class B member 1 [Source:HGNC Symbol;Acc:5258]

Sequence

>retro_meug_1896
AAGACAGAGTATCTGGAAGAGAGGTGAGTTAAGGAGGTTGTAAAGAAGCACTCACAGTTCATTGGCTACCCCATCACACT
TTATTTAATGAAATTATGAGAGAAGGAAATCAGTAATTATGGGACAGAGGAAGACAAAGAGAAAAAAGAAGAGCCAGCTA
AAGATGAGAAGAGCCTCTAGAGTGAAGATGTAAGTTCTGATGAAGAAGATGAGGTCAGGGACAAGAAGAAGACATAGAAG
TCCAAGGAGAAATGCATGGATCAAGAAGAACTGAATGATATCAAACCCATATGGACACATAACTCTAATGACGTCAGCCA
TGAGGAGTATGGTTGGTTTTATAAGAGACTCACCAATGACTGGAAAGATCCATTGGTGGTAAAGCACTTTTCCATCGAAG
GTCAGCTAGAATTTAGATCTCTGTTCTTCAGCTCCCGCTGGGCTCCCTTTGACCTCTTTAAAAACCAAAAGAAGAACATT
AAGCTGAATGTGTTCATCATGGGCAGTCATGATGAGCCTATTCCTGAATATTTTAATTTTATCTGAGGCATGGTGGACTC
TGAGGAGCTGCCCCTCAACATTGCAAGAGAGATACTGCAGCAGAGTAAGATCTTAATGGTCATTTATAAGAACATCATCA
AGAAGTGTCTAGAAGTCTTCTCTCACTGGAAGAAGACAAAGAGAATTACAAAAAAAAAAAGTTCTACGGGGCCTTTTTGA
AAACCTAAAGTTTGGAATCCCTGAGGAATCAAGCAACAGGCACTGTTTATCTGAAGTGTTACATTATCACACATCTTAGT
CAGGAGACGAGATGACTTCCTTGTCTGAATATATGTTTGGAATGAAGAAAACCCAGAGATCCATCTACTATATCAGCAGA
GAG

Alignment

ORF - retro_meug_1896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.72 %
• Parental protein coverage: 52.08 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDETEEDKEKEEEEPAKDEEKPKIEDVGSDEE
          .TEYLEER.VKEVVKKHSQFIGYPITLYL.K..EKEIS...TEEDKEK.EE.PAKDE.....EDV.SDEE
Retrocopy KTEYLEER*VKEVVKKHSQFIGYPITLYLMKL*EKEISNYGTEEDKEKKEE-PAKDEKSL*SEDVSSDEE

Parental  DEGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDISQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEF
          DE..DKKK.T.K.KEK..DQEELN..KPIWT.N..D.S.EEYG.FYK.LTNDW.D.L.VKHFS.EGQLEF
Retrocopy DEVRDKKK-T*KSKEKCMDQEELNDIKPIWTHNSNDVSHEEYGWFYKRLTNDWKDPLVVKHFSIEGQLEF

Parental  RALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSK
          R.L.F..R.APFDLF.N.KK..NIKL....VFIM.S.DE.IPEY.NFI.G.VDSE.LPLNI.RE.LQQSK
Retrocopy RSLFFSSRWAPFDLFKNQKK--NIKL---NVFIMGSHDEPIPEYFNFI*GMVDSEELPLNIAREILQQSK

Parental  ILKVIRKNIVKKCLELFS-ELAEDKENY--KKFYEAFSK-NLKLGIHEDSTNRRRLSELLRYHTSQSGDE
          IL.VI.KNI.KKCLE.FS..L.EDKENY....FY.AF.K.NLK.GI.E.S.NR..LSE.L.YHTS.SGDE
Retrocopy ILMVIYKNIIKKCLEVFS<SLEEDKENYXXXXFYGAFLK<NLKFGIPEESSNRHCLSEVLHYHTS*SGDE

Parental  MTSLSEYVSRMKETQKCIYYITGE
          MTSLSEY...MK.TQ..IYYI..E
Retrocopy MTSLSEYMFGMKKTQRSIYYISRE

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_1896 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1896 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 14 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001981	4 retrocopies	retro_cfam_1108, retro_cfam_411, retro_cfam_562, retro_cfam_881,
Felis catus	ENSFCAG00000009764	1 retrocopy	retro_fcat_1177,
Homo sapiens	ENSG00000096384	2 retrocopies	retro_hsap_2912, retro_hsap_2958,
Gorilla gorilla	ENSGGOG00000008889	2 retrocopies	retro_ggor_1011, retro_ggor_701,
Macropus eugenii	ENSMEUG00000013735	1 retrocopy	retro_meug_1896 ,
Myotis lucifugus	ENSMLUG00000005239	2 retrocopies	retro_mluc_1604, retro_mluc_865,
Macaca mulatta	ENSMMUG00000022686	2 retrocopies	retro_mmul_1319, retro_mmul_1869,
Mus musculus	ENSMUSG00000023944	3 retrocopies	retro_mmus_1916, retro_mmus_3528, retro_mmus_856,
Otolemur garnettii	ENSOGAG00000011961	1 retrocopy	retro_ogar_2574,
Pongo abelii	ENSPPYG00000016655	2 retrocopies	retro_pabe_2425, retro_pabe_415,
Pan troglodytes	ENSPTRG00000018217	4 retrocopies	retro_ptro_1850, retro_ptro_1968, retro_ptro_2003, retro_ptro_880,
Rattus norvegicus	ENSRNOG00000019834	6 retrocopies	retro_rnor_1561, retro_rnor_1562, retro_rnor_1787, retro_rnor_597, retro_rnor_598, retro_rnor_87,
Tupaia belangeri	ENSTBEG00000014873	1 retrocopy	retro_tbel_1428,
Tursiops truncatus	ENSTTRG00000006924	1 retrocopy	retro_ttru_292,