RetrogeneDB ID: retro_cjac_4226

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:141275363..141276103(-)
• Located in intron of: ENSCJAG00000004258

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF622
• Ensembl ID: ENSCJAG00000012047
• Aliases: None
• Description: None

Sequence

>retro_cjac_4226
TGCAGTAAGAAATTTGCCTCTTTCAACACCTACAAAAACTGCTTCAAGTCCTAGCAGCGTGTTGAACTACAGAAGAAGAC
CATGCAGGCTGTGAATAAGAAAGTGGAGATGATGAATGAAAAGAACTTGGACAGGGTGGACAAGGATGCCAGAAATGCAG
TCATCCAGCAGGCCATCAAGGCTCTGCCATCCATGTCTCCCAAAAAGGAGCTCCCAGCACCTGCAGAGGAGTCCAGGAGT
TCCGTGGCCATGGCTGCTGGTGGCCGTGTAACCCATAAGAGAAACCTGACTGAGAAACTGCCCCAGCTCCAGTGGTTTGA
ACAGTGGGTGAAGAAGGTGGCAAGGCAGCAGGAGGAAGACAGTGAGGAGGAAGAGGACCTGGATGAAAATGATTGGGAAG
ATAATGATTCTGACGAAGAATTGTAATGTGAGGATACTGAAGCAATGGATGATGTGGAAGAGCAGGATGGAGAGGAAGAA
GAGGCTGGGGAAAGCCCACCCCTTGGTGCCATCTCTGTAATAGATGGCTTATTTTGTCCCAGTATTCAAGCTCACTCATG
AAGAATGGGGCTTATATGACCAAAGTCTACTGCTTCTTTATTACCAATATAGAATATCTTTCAGATGTTAAGGGACTCAT
TAATTACTTGGGAGAAAAATTTTATGTTGAGAAGATTTGCTTGTGGTGCAATGAGAAAGGGAAGTCCTTCTACTCAACAG
AAGCTGTACAGTCCTATATG

Alignment

ORF - retro_cjac_4226 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.6 %
• Parental protein coverage: 53.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CSKKFASFNAYENHLKSRRHAELEKKAVQAVNRKVEMMNEKNLEKGLGVDGVDKDAMNAAIQQAIKAQPS
          CSKKFASFN.Y.N..KS....EL.KK..QAVN.KVEMMNEKNL.....VD.....A.......A......
Retrocopy CSKKFASFNTYKNCFKS*QRVELQKKTMQAVNKKVEMMNEKNLDR---VDKDARNAVIQQAIKALPSMSP

Parental  MSPKKAPPAPAKEATGDVAVGTGGRRTHDRDPSEKPPRLQWFEQQAKKLAKQQEGSEEEEEDLDEDDWED
          .....AP..........VA...GGR.TH.R...EK.P.LQWFEQ..KK.A.QQE...EEEEDLDE.DWED
Retrocopy KKELPAPAEESRSS---VAMAAGGRVTHKRNLTEKLPQLQWFEQWVKKVARQQEEDSEEEEDLDENDWED

Parental  IDSDEELECEDTEAMDNAAEQDAEEEEAGEKPPLGAIPITDCLFC-SRHSSSLMKNVAHMTKVHSFFIPD
          .DSDEEL.CEDTEAMD...EQD.EEEEAGE.PPLGAI...D.LFC.S..SSSLMKN.A.MTKV..FFI..
Retrocopy NDSDEEL*CEDTEAMDDVEEQDGEEEEAGESPPLGAISVIDGLFC<SQYSSSLMKNGAYMTKVYCFFITN

Parental  IEYLSDIKGLITYLGEKVGVGKICLWCNEKGKSFYSTEAVQAHM
          IEYLSD.KGLI.YLGEK..V.KICLWCNEKGKSFYSTEAVQ..M
Retrocopy IEYLSDVKGLINYLGEKFYVEKICLWCNEKGKSFYSTEAVQSYM

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	0.13 RPM	6.72 RPM
SRP051959_heart	1.37 RPM	11.12 RPM
SRP051959_kidney	0.09 RPM	7.06 RPM
SRP051959_liver	0.22 RPM	6.61 RPM
SRP051959_lung	0.42 RPM	7.29 RPM
SRP051959_lymph_node	0.34 RPM	6.87 RPM
SRP051959_skeletal_muscle	0.44 RPM	8.45 RPM
SRP051959_spleen	0.29 RPM	6.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4226 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4226 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4226 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012047	1 retrocopy	retro_cjac_4226 ,
Rattus norvegicus	ENSRNOG00000049087	1 retrocopy	retro_rnor_2676,
Tupaia belangeri	ENSTBEG00000006779	1 retrocopy	retro_tbel_1283,