RetrogeneDB ID: retro_cjac_1724

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:6217807..6218385(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATXN3
• Ensembl ID: ENSCJAG00000018025
• Aliases: None
• Description: None

Sequence

>retro_cjac_1724
TATCAGAGGCTCAGGATCGATCCTATAAATGAAAGATCATTTATATGCAATTATAAGGAACACTGATTTACAGTTAGAAA
ATTAGGAAAACAGCGGTTTAACTTGAATTCTCTCTTGACGGGTCCAGAATTAATATCAGATACATATCTTGCACTTTTCT
TGGCTCAGTTACAACAGGAAGGTTATTCTATATTTGTTGTTAAGGGTGATCTGCCAGACTGTGAAGCTGACCAACTTCTG
CAGATGATTAGGGTCCAACAGATGCATCGACCAAAACTTACTGGAGAAGAATTAGCACAACTAAAAGAGCAAAGAGTCCA
TAAAACAGACCTGGAACGAGTGTTAGAAGCACATGATGGCTCAGGAATGTTAGATGAAGATGAGGAGGATTTGCAGAGGG
CTCTGGCACTAAACCTCCAAGAAATTGACATGGAAGATGAGGAAGCAGATCTCCACAGGGCTCTTCAGCTAAGTATGCAG
GTAGTTCCAGAAATATATCTCAAGATATTCCACAGACAACAGGTACAAATCTTACTTCAGAAGAGCTTCGGAAGAGACAA
GAAGCCAACTTTGAAAAA

Alignment

ORF - retro_cjac_1724 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.33 %
• Parental protein coverage: 54.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YQRLRIDPINERSFICNYKEHWFTVRKLGKQWFNLNSLLTGPELISDTYLALFLAQLQQEGYSIFVVKGD
          YQRLRIDPINERSFICNYKEH.FTVRKLGKQ.FNLNSLLTGPELISDTYLALFLAQLQQEGYSIFVVKGD
Retrocopy YQRLRIDPINERSFICNYKEH*FTVRKLGKQRFNLNSLLTGPELISDTYLALFLAQLQQEGYSIFVVKGD

Parental  LPDCEADQLLQMIRVQQMHRPKLIGEELAQLKEQRVHKTDLERVLEANDGSGMLDEDEEDLQRALALSRQ
          LPDCEADQLLQMIRVQQMHRPKL.GEELAQLKEQRVHKTDLERVLEA.DGSGMLDEDEEDLQRALAL..Q
Retrocopy LPDCEADQLLQMIRVQQMHRPKLTGEELAQLKEQRVHKTDLERVLEAHDGSGMLDEDEEDLQRALALNLQ

Parental  EIDMEDEEADLRRAIQLSMQ-GSSRNISQDIPQTTGTNLTSEELRKRREAYFEK
          EIDMEDEEADL.RA.QLSMQ.GSSRNISQDIPQTTGTNLTSEELRKR.EA.FEK
Retrocopy EIDMEDEEADLHRALQLSMQ<GSSRNISQDIPQTTGTNLTSEELRKRQEANFEK

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
SRP051959_colon	0.00 RPM	37.45 RPM
SRP051959_heart	0.02 RPM	28.42 RPM
SRP051959_kidney	0.02 RPM	32.77 RPM
SRP051959_liver	0.00 RPM	25.56 RPM
SRP051959_lung	0.00 RPM	45.92 RPM
SRP051959_lymph_node	0.05 RPM	41.66 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.74 RPM
SRP051959_spleen	0.00 RPM	41.11 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1724 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1724 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1724 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,