RetrogeneDB ID: retro_cjac_4069

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:57086321..57087427(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSIP1
• Ensembl ID: ENSCJAG00000012471
• Aliases: None
• Description: None

Sequence

>retro_cjac_4069
ATGACTAGTGATTTCAAATCTGTAGACCTCATCTTCACCAAGATGAAAGGTTGTCCCCATTGACCAGCTCGAGTAGATGA
AGTTTATGATGGAGCTATAAAGCCAACTACAAACAAACTACCCATTTTCTTTTTTGGAACCCATGAGACTGCTTTTTTAG
GACCAAAGGATATATTTCCTTACTTCAAAAATAAGGAAGAGCATAACAAACCAAATAAAAGAAAAGGTTTTAATGAAGAT
TTATGGGAGACAGATAACAATACAAAAGTGAAATTTTCAAGTCGACAGGCAGCAACTGAACAATCAAATGCATCATCTGA
TGTTGAAGTTGAAGAAAAGGAAACCAGTGTTTCAAAGGAAGATACCATGAAGTAAAGGCCAGACATGAGGATGTGACTAA
AGCAGTTGACATAACTAGTCCGAAAGCTGCCAGAGGAGAAAGAGAAAGACAGAAAAACAAGTAGAAACTGAGAGTGCAGG
AGTAGTGACAACAGCAACAGCATCTGTTAATCTAAAAGTGAGTCCTAAAAGAGGATGACCTGCAGCTACAGAAGTCAAGA
TTCCAAAACCAAGAGGCAGACCCAAAGTGGTTAAACAGTTCTGTCCTTCAGATAGTGACATTGTTACTGAAGAGGACAAA
AGAAAAAGGGTTAAGAGGAAAAACAACCTAAAAAGCAGCTTAATAAGGAGGAAGAGGGCCAGAAGGAAGAAGATAAGCCA
AGAAAATAGCCAGAGAAAAAAGAGAGGAAGAAAGAAGTTGAATCAAAAAGGAAAAATTTAGCTAAAACAGGGGTATGTCA
ACCTCTGATTCTGAAGAAGAAGGATATGATCAAGAAGGTGAAAAGAAGAGAAAAGGTGGGAGGAACTTTCAGACAACTCA
CAGAAGGAATATGCTGAAAGGCCAACATGAGACAGAAGTGGCAGATCGAAAATGCAAGTGAGAGGAACAAGTGGAAACTG
AGCAGTGGAATAAAGATGAAGGAAAGAAGCCAGAAGATAAGAAAGTGGAGAAGTGAGAAACATCAATGGATTCTCGACTT
CAAAGGGTACATGCTGAGATTAATAATTCACTCAAAATTGATAATCTTGATGTGTACAGATGCATC

Alignment

ORF - retro_cjac_4069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.19 %
• Parental protein coverage: 70.57 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MTRDFKPGDLIFAKMKGYPHWPARVDEVPDGAVKPPTNKLPIFFFGTHETAFLGPKDIFPYSENKEKYGK
          MT.DFK..DLIF.KMKG.PH.PARVDEV.DGA.KP.TNKLPIFFFGTHETAFLGPKDIFPY..NKE...K
Retrocopy MTSDFKSVDLIFTKMKGCPH*PARVDEVYDGAIKPTTNKLPIFFFGTHETAFLGPKDIFPYFKNKEEHNK

Parental  PNKRKGFNEGLWEIDNNPKVKFSSQQAATKQSNASSDVEVEEKETSVSKEDTD-HEEKASNEDMTKAVDI
          PNKRKGFNE.LWE.DNN.KVKF.S...A.......S.....E............HE.KA..ED.TKAVDI
Retrocopy PNKRKGFNEDLWETDNNTKVKF-SSRQAATEQSNASSDVEVEEKETSVSKEDT<HEVKARHEDVTKAVDI

Parental  TTPKAARRG-RKRKAEKQVETEEAGVVTTATASVNLKVSPKRGRPAATEVKIPKPRGRPKVVKQPCPSES
          T.PKAA.RG.RKRK.EKQVETE.AGVVTTATASVNLKVSPKRG.PAATEVKIPKPRGRPKVVKQ.CPS.S
Retrocopy TSPKAA-RG<RKRKTEKQVETESAGVVTTATASVNLKVSPKRG*PAATEVKIPKPRGRPKVVKQFCPSDS

Parental  DIITEEDK-SKKKGQEEKQPKKQFKKEEEGQKEEDKPRKEPDKKEGKKEVESKRKNLAKTGV-TSTSDSE
          DI.TEEDK..KK...E....K.Q..KEEEGQKEEDKPRK.P.KKE.KKEVESKRKNLAKTGV..STSDSE
Retrocopy DIVTEEDK<KKKG*EEKQPKK-QLNKEEEGQKEEDKPRK*PEKKERKKEVESKRKNLAKTGV<MSTSDSE

Parental  EEGDDQEGEKKRKGGRNFQAAHRRNMLKGQHEKEAADRKRKQEEQMETEQQNKDEGKKPEVKKVEKKRET
          EEG.DQEGEKKRKGGRNFQ..HRRNMLKGQHE.E.ADRK.K.EEQ.ETEQ.NKDEGKKPE.KKVE.K.ET
Retrocopy EEGYDQEGEKKRKGGRNFQTTHRRNMLKGQHETEVADRKCK*EEQVETEQWNKDEGKKPEDKKVE-K*ET

Parental  SMDSRLQRIHAEIKNSLKIDNLDVNRCI
          SMDSRLQR.HAEI.NSLKIDNLDV.RCI
Retrocopy SMDSRLQRVHAEINNSLKIDNLDVYRCI

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	0.16 RPM	30.20 RPM
SRP051959_heart	0.60 RPM	45.83 RPM
SRP051959_kidney	0.73 RPM	38.05 RPM
SRP051959_liver	0.04 RPM	20.21 RPM
SRP051959_lung	0.29 RPM	57.68 RPM
SRP051959_lymph_node	0.23 RPM	70.89 RPM
SRP051959_skeletal_muscle	0.13 RPM	27.10 RPM
SRP051959_spleen	0.36 RPM	53.45 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4069 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4069 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4069 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006157	2 retrocopies	retro_cjac_338, retro_cjac_4022,
Callithrix jacchus	ENSCJAG00000012471	1 retrocopy	retro_cjac_4069 ,
Callithrix jacchus	ENSCJAG00000015775	1 retrocopy	retro_cjac_4165,
Homo sapiens	ENSG00000164985	1 retrocopy	retro_hsap_4136,
Mus musculus	ENSMUSG00000028484	1 retrocopy	retro_mmus_2896,
Pan troglodytes	ENSPTRG00000020786	1 retrocopy	retro_ptro_2811,
Tupaia belangeri	ENSTBEG00000000715	1 retrocopy	retro_tbel_364,