RetrogeneDB ID: retro_hsap_89

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:13336985..13338053(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000123594
• Aliases: ATXN3L, MJDL
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ATXN3
• Ensembl ID: ENSG00000066427
• Aliases: ATXN3, AT3, ATX3, JOS, MJD, MJD1, SCA3
• Description: ataxin 3 [Source:HGNC Symbol;Acc:7106]

Sequence

>retro_hsap_89
ATGGATTTCATCTTTCATGAGAAACAGGAAGGTTTCCTGTGTGCTCAGCACTGTCTGAACAATCTATTGCAAGGAGAATA
TTTTAGCCCTGTGGAATTAGCCTCAATTGCACATCAGCTAGATGAAGAAGAGAGGATGAGAATGGCAGAAGGAGGAGTCA
CCAGTGAAGAGTATCTTGCATTTTTACAGCAGCCTTCAGAAAACATGGATGATACCGGTTTCTTCTCCATTCAGGTAATA
AGCAATGCCTTGAAGTTCTGGGGTTTAGAGATCATCCATTTCAATAATCCTGAATATCAGAAGCTCGGCATTGATCCTAT
AAATGAAAGATCTTTTATATGTAATTATAAACAACACTGGTTTACTATTAGAAAATTTGGAAAACACTGGTTTAACTTGA
ATTCTCTCTTGGCGGGTCCAGAATTAATATCAGATACATGCCTTGCAAATTTCTTGGCTCGATTACAACAACAAGCATAT
TCTGTATTTGTTGTCAAGGGTGATCTGCCAGACTGTGAAGCTGACCAACTCCTGCAGATCATCAGTGTCGAAGAGATGGA
TACACCAAAACTTAATGGAAAAAAATTAGTAAAACAAAAAGAGCATAGAGTCTATAAAACAGTCCTTGAAAAAGTATCAG
AAGAAAGTGATGAGTCTGGAACATCAGACCAAGATGAGGAGGATTTTCAGAGGGCCCTTGAACTAAGCCGCCAAGAAACC
AATAGAGAAGATGAACATCTCCGCAGTACTATTGAGTTAAGCATGCAAGGTAGTTCCGGAAACACATCGCAAGATCTTCC
AAAGACATCATGTGTAACTCCTGCTTCAGAACAGCCGAAGAAAATAAAAGAAGACTATTTTGAAAAGCATCAGCAGGAAC
AGAAGCAGCAGCAACAACAGTCAGATCTGCCGGGCCACAGTTCATACCTACACGAAAGGCCAACAACAAGTTCGAGAGCA
ATTGAGAGTGATCTCAGTGATGACATCAGTGAAGGCACAGTACAGGCCGCTGTCGACACCATTTTAGAAATTATGAGAAA
GAATTTGAAAATCAAAGGGGAAAAATAA

Alignment

ORF - retro_hsap_89 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESIFHEKQEGSLCAQHCLNNLLQGEYFSPVELSSIAHQLDEEERMRMAEGGVTSEDYRTFLQQPSGNMD
          M..IFHEKQEG.LCAQHCLNNLLQGEYFSPVEL.SIAHQLDEEERMRMAEGGVTSE.Y..FLQQPS.NMD
Retrocopy MDFIFHEKQEGFLCAQHCLNNLLQGEYFSPVELASIAHQLDEEERMRMAEGGVTSEEYLAFLQQPSENMD

Parental  DSGFFSIQVISNALKVWGLELILFNSPEYQRLRIDPINERSFICNYKEHWFTVRKLGKQWFNLNSLLTGP
          D.GFFSIQVISNALK.WGLE.I.FN.PEYQ.L.IDPINERSFICNYK.HWFT.RK.GK.WFNLNSLL.GP
Retrocopy DTGFFSIQVISNALKFWGLEIIHFNNPEYQKLGIDPINERSFICNYKQHWFTIRKFGKHWFNLNSLLAGP

Parental  ELISDTYLALFLAQLQQEGYSIFVVKGDLPDCEADQLLQMIRVQQMHRPKLIGEELAQLKEQRVHKTDLE
          ELISDT.LA.FLA.LQQ..YS.FVVKGDLPDCEADQLLQ.I.V..M..PKL.G..L...KE.RV.KT.LE
Retrocopy ELISDTCLANFLARLQQQAYSVFVVKGDLPDCEADQLLQIISVEEMDTPKLNGKKLVKQKEHRVYKTVLE

Parental  RVLEANDGSGMLDEDEEDLQRALALSRQEIDMEDEEADLRRAIQLSMQGSSRNISQDMTQTSGTNLTSEE
          .V.E..D.SG..D.DEED.QRAL.LSRQE...EDE...LR..I.LSMQGSS.N.SQD...TS.....SE.
Retrocopy KVSEESDESGTSDQDEEDFQRALELSRQETNREDEH--LRSTIELSMQGSSGNTSQDLPKTSCVTPASEQ

Parental  LRKRREAYFEKQQQKQQQQQQQQQQGDLSGQSSHPCERPATSSGALGSDLGDAMSEEDMLQAAVTMSLET
          ..K..E.YFEK.QQ.Q.QQQQQ....DL.G.SS...ERP.TSS.A..SDL.D..S.E...QAAV...LE.
Retrocopy PKKIKEDYFEKHQQEQKQQQQQ---SDLPGHSSYLHERPTTSSRAIESDLSDDIS-EGTVQAAVDTILEI

Parental  VRNDLKTEGKK
          .R..LK..G.K
Retrocopy MRKNLKIKGEK

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.00 RPM	18.33 RPM
bodymap2_adrenal	0.00 RPM	28.94 RPM
bodymap2_brain	0.00 RPM	16.71 RPM
bodymap2_breast	0.00 RPM	39.61 RPM
bodymap2_colon	0.00 RPM	21.98 RPM
bodymap2_heart	0.00 RPM	13.00 RPM
bodymap2_kidney	0.00 RPM	21.61 RPM
bodymap2_liver	0.00 RPM	6.67 RPM
bodymap2_lung	0.00 RPM	17.95 RPM
bodymap2_lymph_node	0.00 RPM	29.16 RPM
bodymap2_ovary	0.00 RPM	27.22 RPM
bodymap2_prostate	0.00 RPM	28.23 RPM
bodymap2_skeletal_muscle	0.00 RPM	5.35 RPM
bodymap2_testis	2.85 RPM	35.63 RPM
bodymap2_thyroid	0.00 RPM	20.34 RPM
bodymap2_white_blood_cells	0.00 RPM	42.25 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_89 was not detected

EST

No EST(s) were mapped for retro_hsap_89 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_197301	1826 libraries	2 libraries	1 library	0 libraries	0 libraries

The graphical summary, for retro_hsap_89 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_89 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_89 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005786	2 retrocopies	retro_btau_1652, retro_btau_330,
Choloepus hoffmanni	ENSCHOG00000005302	1 retrocopy	retro_chof_2238,
Callithrix jacchus	ENSCJAG00000018025	2 retrocopies	retro_cjac_1724, retro_cjac_375,
Cavia porcellus	ENSCPOG00000010887	1 retrocopy	retro_cpor_1460,
Homo sapiens	ENSG00000066427	1 retrocopy	retro_hsap_89 ,
Macaca mulatta	ENSMMUG00000020751	1 retrocopy	retro_mmul_298,
Monodelphis domestica	ENSMODG00000002006	2 retrocopies	retro_mdom_1498, retro_mdom_1573,
Nomascus leucogenys	ENSNLEG00000017126	1 retrocopy	retro_nleu_66,
Pongo abelii	ENSPPYG00000006075	1 retrocopy	retro_pabe_9,
Tupaia belangeri	ENSTBEG00000008099	3 retrocopies	retro_tbel_102, retro_tbel_2635, retro_tbel_3925,