RetrogeneDB ID: retro_cjac_3262

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:10045297..10045756(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: QKI
• Ensembl ID: ENSCJAG00000012368
• Aliases: None
• Description: QKI, KH domain containing, RNA binding [Source:HGNC Symbol;Acc:21100]

Sequence

>retro_cjac_3262
CTGCTGGATGGAGAAATTAGCGGAGTACGGAAAGACATGTACAATGACACATTAAATGTCAGTACAGAGAAAAGGAGTGC
AGAATTGCCTGATGCTGTGGGACCTATTGTTCAGTTACAAGAGAAATCTTATGTGCCTGTAAAAGAATACCCAGATTTTA
ATTTTGTTGGGCGAACTCTTGGACCTAGAGGACTTACAGCCAAACAACTTGAAGCAGAGACGGGATGTAAAATAATGGTC
CAAGGCAAAGGCTAAATGAGGGATTTAAAAAAGGAGGAGCAAAATAGAGGCAAGCCCAACTGGGAGCATCTACATGAAGA
TTTACATGTACTAATCACTGTGGAAGATGCTAAGAACAGAGCAGAAATCAAACTGAAGAGAGCAGTTGAAGAAGTAAAGA
AATTATTGGTACCTGCAGCAGAAGGAGAAGACAGCCTGAAGATGCAGCTGATGCAACTC

Alignment

ORF - retro_cjac_3262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.56 %
• Parental protein coverage: 50.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLLTEISRVRKDMYNDTLNGSTEKRSAELPDAVGPIVQLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQL
          LL..EIS.VRKDMYNDTLN.STEKRSAELPDAVGPIVQLQEK.YVPVKEYPDFNFVGR.LGPRGLTAKQL
Retrocopy LLDGEISGVRKDMYNDTLNVSTEKRSAELPDAVGPIVQLQEKSYVPVKEYPDFNFVGRTLGPRGLTAKQL

Parental  EAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAEIKLKRAVEEVKKLLVPAA
          EAETGCKIMV.GKG.MRD.KKEEQNRGKPNWEHL.EDLHVLITVEDA.NRAEIKLKRAVEEVKKLLVPAA
Retrocopy EAETGCKIMVQGKG*MRDLKKEEQNRGKPNWEHLHEDLHVLITVEDAKNRAEIKLKRAVEEVKKLLVPAA

Parental  EGEDSLKKMQLMEL
          EGEDSLK.MQLM.L
Retrocopy EGEDSLK-MQLMQL

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	23.01 RPM
SRP051959_heart	0.18 RPM	168.25 RPM
SRP051959_kidney	0.09 RPM	62.83 RPM
SRP051959_liver	0.04 RPM	57.12 RPM
SRP051959_lung	0.15 RPM	122.93 RPM
SRP051959_lymph_node	0.02 RPM	52.30 RPM
SRP051959_skeletal_muscle	0.15 RPM	115.39 RPM
SRP051959_spleen	0.06 RPM	91.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3262 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3262 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3262 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002780	1 retrocopy	retro_cjac_1930,
Callithrix jacchus	ENSCJAG00000006580	1 retrocopy	retro_cjac_1185,
Callithrix jacchus	ENSCJAG00000012368	1 retrocopy	retro_cjac_3262 ,
Macaca mulatta	ENSMMUG00000000428	1 retrocopy	retro_mmul_642,