RetrogeneDB ID: retro_btau_330

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:8893214..8894087(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATXN3
• Ensembl ID: ENSBTAG00000005786
• Aliases: None
• Description: ataxin-3 [Source:RefSeq peptide;Acc:NP_001092686]

Sequence

>retro_btau_330
ATGGAGTCCATCTTCCACGAAAAACAAGAAGGCTCACTTTGTGCTCAACATTGCTTGAATAACCTACTGCAAGGAGAATA
CTTCAGCCCTGTGGAATCATCTTCAATTGCACATCAGCTAGATGAGGAAGAGAGGATGAGAATGGCAGAAGGAGGAGTTA
CTAGTGAAGACTATCGCACATTTTTGCAGCAGCCTTCTGGAAATATGGATGACAGTGGCTTTTTCTCTATTCAAGTTATA
AGCAATGCCTTGAAAGTTTGGGGTTTAGAACTAATCCTGTTTAACAGTCCAGAGTACCAGAGGCTCAGGATTGATCCCAT
AAATGAAAGATCATTTATATGCAACTATAAAGAACACTGGTTTACAGTTAGAAAATTAGGAAAACAGTGGTTCAACTTGA
ATTCTCTTTTGACGGGTCCAGAATTAATATCAGACACATACCTTGCACTTTTCTTGGCTCAGTTACAACAGGAAGGTTAC
TCTATATTTGTTGTTAAGGGTGATCTGCCAGATTGCGAAGCTGACCAACTTCTACAGATGATCAGGGTCCAACAGACGCA
TCAACCAAAACTTATTGGAGAAGAATTAGCACAACTTAAAGAACAGAGAGTCCAGAAAACAGATCTAGAACACGTCTTAG
AAGTAAATGATGGGACAGGAATGTTAGAAGAGGATGAGGAGGAATTGCAGAGGGCTCTGGCACTAAGTCGCCAAGAAATT
GACATGGAAGATGAAGAAGCCGATCTCCCCAGGGCCATTCAGCTCAGTATGCAAGGTACTTCCAGAAATAGATGACAAGA
TATCCCACAGACATCGGGTTCACATCCTACTTCAGAAGAGCTACGGAAAAGAAGAGAAGCCTACTTTGAAAAG

Alignment

ORF - retro_btau_330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.6 %
• Parental protein coverage: 79.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESIFHEKQEGSLCAQHCLNNLLQGEYFSPVELSSIAHQLDEEERMRMAEGGVTSEDYRTFLQQPSGNMD
          MESIFHEKQEGSLCAQHCLNNLLQGEYFSPVE.SSIAHQLDEEERMRMAEGGVTSEDYRTFLQQPSGNMD
Retrocopy MESIFHEKQEGSLCAQHCLNNLLQGEYFSPVESSSIAHQLDEEERMRMAEGGVTSEDYRTFLQQPSGNMD

Parental  DSGFFSIQQVISNALKVWGLELILFNSPEYQRLRIDPINERSFICNYKEHWFTVRKLGKQWFNLNSLLTG
          DSGFFSI.QVISNALKVWGLELILFNSPEYQRLRIDPINERSFICNYKEHWFTVRKLGKQWFNLNSLLTG
Retrocopy DSGFFSI-QVISNALKVWGLELILFNSPEYQRLRIDPINERSFICNYKEHWFTVRKLGKQWFNLNSLLTG

Parental  PELISDTYLALFLAQLQQEGYSIFVVKGDLPDCEADQLLQMIRVQQMHRPKLIGEELAQLKEQRVQKTDL
          PELISDTYLALFLAQLQQEGYSIFVVKGDLPDCEADQLLQMIRVQQ.H.PKLIGEELAQLKEQRVQKTDL
Retrocopy PELISDTYLALFLAQLQQEGYSIFVVKGDLPDCEADQLLQMIRVQQTHQPKLIGEELAQLKEQRVQKTDL

Parental  EHVLEVNDGTGMLDEDEEELQRALALSRQEIDMEDEEADLRRAIQLSMQGTSRNRCQDIPQTSGSHPTSE
          EHVLEVNDGTGML.EDEEELQRALALSRQEIDMEDEEADL.RAIQLSMQGTSRNR.QDIPQTSGSHPTSE
Retrocopy EHVLEVNDGTGMLEEDEEELQRALALSRQEIDMEDEEADLPRAIQLSMQGTSRNR*QDIPQTSGSHPTSE

Parental  ELRKRREAYFEK
          ELRKRREAYFEK
Retrocopy ELRKRREAYFEK

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
ERP005899_liver	0.22 RPM	2.81 RPM
ERP005899_muscle	0.26 RPM	5.65 RPM
SRP017611_brain	0.05 RPM	3.33 RPM
SRP017611_kidney	0.30 RPM	5.81 RPM
SRP017611_liver	0.23 RPM	2.19 RPM
SRP030211_testis	7.60 RPM	80.91 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_330 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_330 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_330 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 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,
Pteropus vampyrus	ENSPVAG00000015316	2 retrocopies	retro_pvam_1201, retro_pvam_587,
Tupaia belangeri	ENSTBEG00000008099	3 retrocopies	retro_tbel_102, retro_tbel_2635, retro_tbel_3925,