RetrogeneDB ID: retro_cjac_375

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:11295691..11296753(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023329
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_cjac_375
ATGGAGCTCATCTTCCACGAGAAACAAGAAGGATCCCTCTGTGCCCAGCACTGCCTGAATAATCTATTGCAAGGTGAATA
TTTTACCGCTGTGGAATTAGCCTCAATTGCACACCAGCTCGATGAGGAAGAGAGGATGAGAATGGCAGAAGGAGGAGTCA
CCAGTGAAGACTATCGCGCATTTTTACAGCAGCCTTCAGGAAACATGGATGACACAGGTTTCTTTTCTATTCAGGTCATA
ACCAATGCCTTGAAGTTCTGGGGTTTAGATGTGATCCCTTTAAACAGCTCTGCCTATCAAAAGCTTGGGATTAATCCTAT
AAATGAAAGATCTTTTATAGGTAATTATGAACAACACTGGTTTACTCTTAGAAAATTTGGAAAACTCTGGTTTAATTTGG
ATTCTCTCTTGGCGGGCCCAGTATTAATATCAGATACATACCTCGTGCTATTCCTGAGTAAACTGAGAAAGGAAGGCTAC
TCTGTATTTGTTGTTAAGGGTGATCTGCCAGACTGTGAAGCTGACCAATTCCTGCAGACCATCAGGGTCAAAGAAATAGA
TCACCCAAAACTTACTGAAAGAAAACTACCACAAGAAAAACAACAAAGAGACCATAAAACAGTCCTTAAAAAAGCGTCAG
AAGAAACTGATGAATCCGACCTATCAGATGAAGATGAGGATTTTCAGAGGGCCCTAGCACTGAGTCGACAAGAAAGGAAG
AGAGAAGATGAAGATCTTCACAGGGCTATTAAATTAAGCATGCAAGGTACTTCTGGAAACATATCGCAAGATCTTCCACA
GACATCGTGTGTAACTCCTGCTTTGGAAGAGCTGAAGAAAATAAAAGACTGTTTTGAAAAGCATGAGCAAGAACAACAGC
AGAGGAAACAAAAGTCAGATCCGCCAGGTCACAGTTCATGTCTACCCGATACACCGACAACAAGTCTGAGAGGAACTGAC
GGTGATCTCAGTGATGACAGCAACGAAGACATGATCCAGGCCACTGTCGACATGGTTATAGAAGCTGTCAGAAATAACTT
GAAAATCAATGGAGAAAAGTAA

Alignment

ORF - retro_cjac_375 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.37 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESIFHEKQEGSLCAQHCLNNLLQGEYFSPVELSSIAHQLDEEERMRMAEGGVTSEDYRTFLQQPSGNMD
          ME.IFHEKQEGSLCAQHCLNNLLQGEYF..VEL.SIAHQLDEEERMRMAEGGVTSEDYR.FLQQPSGNMD
Retrocopy MELIFHEKQEGSLCAQHCLNNLLQGEYFTAVELASIAHQLDEEERMRMAEGGVTSEDYRAFLQQPSGNMD

Parental  DSGFFSIQVISNALKVWGLELILFNSPEYQRLRIDPINERSFICNYKEHWFTVRKLGKQWFNLNSLLTGP
          D.GFFSIQVI.NALK.WGL..I..NS..YQ.L.I.PINERSFI.NY..HWFT.RK.GK.WFNL.SLL.GP
Retrocopy DTGFFSIQVITNALKFWGLDVIPLNSSAYQKLGINPINERSFIGNYEQHWFTLRKFGKLWFNLDSLLAGP

Parental  ELISDTYLALFLAQLQQEGYSIFVVKGDLPDCEADQLLQMIRVQQMHRPKLIGEELAQLKEQRVHKTDLE
          .LISDTYL.LFL..L..EGYS.FVVKGDLPDCEADQ.LQ.IRV.....PKL....L.Q.K.QR.HKT.L.
Retrocopy VLISDTYLVLFLSKLRKEGYSVFVVKGDLPDCEADQFLQTIRVKEIDHPKLTERKLPQEKQQRDHKTVLK

Parental  RVLEANDGSGMLDEDEEDLQRALALSRQEIDMEDEEADLRRAIQLSMQGSSRNISQDIPQTTGTNLTSEE
          ...E..D.S...DED.ED.QRALALSRQE...EDE..DL.RAI.LSMQG.S.NISQD.PQT.......EE
Retrocopy KASEETDESDLSDED-EDFQRALALSRQERKREDE--DLHRAIKLSMQGTSGNISQDLPQTSCVTPALEE

Parental  LRKRREAYFEKSENKRLIAESELLSGDPSGQSSHPCERPTTSSGALGNDLGDAMSEEDMLQAAVTMSLET
          L.K.....FEK.E.............DP.G.SS.....PTTS......DL.D..S.EDM.QA.V.M..E.
Retrocopy LKKIKDC-FEKHEQEQ---QQRKQKSDPPGHSSCLPDTPTTSLRGTDGDLSDD-SNEDMIQATVDMVIEA

Parental  VKNDLKAEGKK
          V.N.LK..G.K
Retrocopy VRNNLKINGEK

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	0.02 RPM	37.45 RPM
SRP051959_heart	0.11 RPM	28.42 RPM
SRP051959_kidney	0.02 RPM	32.77 RPM
SRP051959_liver	0.00 RPM	25.56 RPM
SRP051959_lung	0.03 RPM	45.92 RPM
SRP051959_lymph_node	0.00 RPM	41.66 RPM
SRP051959_skeletal_muscle	0.02 RPM	10.74 RPM
SRP051959_spleen	0.08 RPM	41.11 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_375 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_375 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_375 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,