RetrogeneDB ID: retro_cjac_478

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:156684009..156684846(+)
• Located in intron of: ENSCJAG00000017843

Retrocopy information

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

Parental gene information

• Parental gene symbol: GK5
• Ensembl ID: ENSCJAG00000001924
• Aliases: None
• Description: None

Sequence

>retro_cjac_478
CAAAAGGCAGCTGAAGAAGAAAATTGTTGTTTTGAGACTATTGATACCTGGCTGTTATATAAGCTCACAAAAGGTTCTGT
ATATGCCATAGATTTTTCAAATGCTAGTACAACTGGACATTTTGACCCATATTAGATGTGTTGGAGTGGGATCATTACCT
CCTTAATTTCAGTACCATTTCTCTTGTACCTCCTGTGAGGGACATAAGCCACAATTTTGGATCCTGGAGGAAGAGATATC
TGGTGTGCCTGTACCACTAGGTGCCTTGGTTGCCGACCAGCAATCAGCCATGTTTGGAGAGGTGATGTGAAACTTCCAGA
CAGGTGATGTGAAACTGACCATGGGAACTGGGACATTTTTGGATATTAACACTGGAAAAAGCCTTCAACAGACTACTGAA
AGTTTTTATCCATTAATTCGGTGAAAGATAGGGCAAGAAGTCATATGCTTAGGTGAAAGCAAGCAGGAGACACTGGTACT
GCCACAAAAGGGACTTAACAGTTAGAGCTTTTCACAGATGCTGCTGAGACTGAAAAAATGGCCAAAAGTGCAGAGGATTC
TGAAGGAGTTTGTTTTGTTCCATCTTCTAGTGGATTACAGGCTCTATTAAATGACCTCTGGGCATATGCCTCTTTTATGG
GGTTTGAAGCCTTCCACCAGTAATTACTAGCTCTTAAGAGCAATATTGAAGTCAGTAGCTTTCAGAAATAGTTATATGAG
ATGATGCAGAAAGAGATTCATACACCTGTAAGAAAAATGTGGGCAGATGGAGGAGTCTGTAAGAACGATTTTGTCATGCA
GATGACTTCAGACCTGATTAAAGAGAATATAGGCAGA

Alignment

ORF - retro_cjac_478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.62 %
• Parental protein coverage: 52.74 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QKAVEEENCCFGTVDTWLLHKLTKGSVYATDFSNASTTGLFDPYKMCWSGMITSLISIP-LSLLPPVRDT
          QKA.EEENCCF.T.DTWLL.KLTKGSVYA.DFSNASTTG.FDPY.MCWSG.ITSLIS.P..SL.PPVRD.
Retrocopy QKAAEEENCCFETIDTWLLYKLTKGSVYAIDFSNASTTGHFDPY*MCWSGIITSLISVP<ISLVPPVRDI

Parental  SHNFGS-VDEEIFGVPIPIVALVADQQSAMFGECC--FQTGDVKLTMGTGTFLDINTGNSPQQTIGGFYP
          SHNFGS...EEI.GVP.P..ALVADQQSAMFGE....FQTGDVKLTMGTGTFLDINTG.S.QQT...FYP
Retrocopy SHNFGS<LEEEISGVPVPLGALVADQQSAMFGEVM*NFQTGDVKLTMGTGTFLDINTGKSLQQTTESFYP

Parental  LIGWKIGQEVVCLAESN-AGDTGTAIKWAQQLDLFTDAAETEKMAKSLEDSEGVCFVPSFSGLQAPLNDP
          LI..KIGQEV.CL.ES..AGDTGTA.K...QL.LFTDAAETEKMAKS.EDSEGVCFVPS.SGLQA.LND.
Retrocopy LIR*KIGQEVICLGESK<AGDTGTATKGT*QLELFTDAAETEKMAKSAEDSEGVCFVPSSSGLQALLNDL

Parental  WACASFMG-LKPSTSKYHLVRAILESI-AFRNKQLYEMMQKEIHIPVTKIRADGGVCKNSFIMQMTSDLI
          WA.ASFMG.LKPSTS.Y.L.RAIL.S...F..K.LYEMMQKEIH.PV.K..ADGGVCKN.F.MQMTSDLI
Retrocopy WAYASFMG>LKPSTSNY*LLRAILKSV<SFQ-K*LYEMMQKEIHTPVRKMWADGGVCKNDFVMQMTSDLI

Parental  NENIDR
          .ENI.R
Retrocopy KENIGR

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	1.35 RPM	22.21 RPM
SRP051959_heart	0.67 RPM	7.84 RPM
SRP051959_kidney	1.58 RPM	11.65 RPM
SRP051959_liver	2.38 RPM	7.21 RPM
SRP051959_lung	0.59 RPM	16.12 RPM
SRP051959_lymph_node	0.55 RPM	12.63 RPM
SRP051959_skeletal_muscle	0.83 RPM	2.23 RPM
SRP051959_spleen	0.78 RPM	10.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_478 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_478 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_478 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001924	1 retrocopy	retro_cjac_478 ,
Callithrix jacchus	ENSCJAG00000007633	3 retrocopies	retro_cjac_125, retro_cjac_3161, retro_cjac_4035,