RetrogeneDB ID: retro_cjac_513

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:32724677..32725308(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIAA1704
• Ensembl ID: ENSCJAG00000019204
• Aliases: None
• Description: KIAA1704 [Source:HGNC Symbol;Acc:20298]

Sequence

>retro_cjac_513
ATGGCAAGGGACCTGATCAGACTGGCCCTGCTGCTTGGCTTCAAGGTCTCGGGAACAGCAGAGGATGAGGAGCGGGACCC
AAGCCCCATTGCAGGACCAGCTCTAATTACTAATTATAAAAGCAGTAGTTCAGATTCATCAGACAGCAATGAAGACAGTA
GTTCTTTGTACAACAAAGGAAATAAAGAATGTGAGGAAGATGACACTGGTCCAACTGAAAGAAAACAGGAAAGATCAGTA
TGATGACAATGATGAAGATGATGATGGGTTTTTTGGACCAGCCCTTCCTCCTGGATTTTAAAAGCAGGATGATTTTCCTC
CAAGGCCTATAATAGGTCCTGCATTGCCACCTGGTTTCATTAAATCTACACAGAAACGTAATGAGCAGAGATGATCCAGG
GCAAAAGGAAACAGAGAGCAGTGAAGATGAGGACATTGTTGGACCATTGCCCACAGAAGGACCAGTTAACTATAATGTAA
AGACAGAATTTGAAAAAAGATCCCAGAGAATGAAAGAAAAACTGACCAAGGAGATGATGATTCTTCTAATCCCATTGTAA
GAGAGTCATAGATGACTGAACTTCCTCCAGAAATGAAAGACTTTGGTCTTGGGCCAAGGACTTTTAAGAGA

Alignment

ORF - retro_cjac_513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.1 %
• Parental protein coverage: 62.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MARDLIGPALPPGFKARGTAEDEERDPSPVAGPALPPNYKSSSSDSSDSDEDSSSLYEEGNQESEDDDTG
          MARDLI..AL..GFK..GTAEDEERDPSP.AGPAL..NYKSSSSDSSDS.EDSSSLY..GN.E.E.DDTG
Retrocopy MARDLIRLALLLGFKVSGTAEDEERDPSPIAGPALITNYKSSSSDSSDSNEDSSSLYNKGNKECEEDDTG

Parental  PTARKQRKN-QDDDEDDDDGFFGPALPPGFKKQDDSPPRPMIGPALPPGFIKATRKSDKGR-DDPEQQET
          PT.RKQ.....DD...DDDGFFGPALPPGF.KQDD.PPRP.IGPALPPGFIK.T.K....R.D......T
Retrocopy PTERKQERS>YDDNDEDDDGFFGPALPPGF*KQDDFPPRPIIGPALPPGFIKSTQKRNEQR>DPGQKE-T

Parental  DSSEDEDIVGPMPAKGPVNYNVTTEFEKRAQRMKEKLTK-GDDDSSKPIVRESWMTELPPEMKDFGLGPR
          .SSEDEDIVGP.P..GPVNYNV.TEFEKR.QRMKEKLTK.GDDDSS.PIVRES.MTELPPEMKDFGLGPR
Retrocopy ESSEDEDIVGPLPTEGPVNYNVKTEFEKRSQRMKEKLTK<GDDDSSNPIVRES*MTELPPEMKDFGLGPR

Parental  TFKR
          TFKR
Retrocopy TFKR

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	5.57 RPM
SRP051959_heart	0.00 RPM	5.93 RPM
SRP051959_kidney	0.00 RPM	9.27 RPM
SRP051959_liver	0.00 RPM	6.58 RPM
SRP051959_lung	0.00 RPM	9.70 RPM
SRP051959_lymph_node	0.00 RPM	8.36 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.18 RPM
SRP051959_spleen	0.00 RPM	9.64 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_513 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_513 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_513 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019204	1 retrocopy	retro_cjac_513 ,
Otolemur garnettii	ENSOGAG00000012513	1 retrocopy	retro_ogar_349,