RetrogeneDB ID: retro_cjac_540

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:70649131..70650184(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELF2
• Ensembl ID: ENSCJAG00000003174
• Aliases: None
• Description: None

Sequence

>retro_cjac_540
GAGGCGTCAACTGAGGAGTCTGAACCAATACATACCTCTCCTATTCCTACGTCACCAAATAGCCATGAACCAATGAAAAA
GAAAAAAGTTGGCCATGAAGCAAAGATCCAACACTCACCAATTTCCCGTGGGTCCCCTCAGTTAGGCATAAAAAGGAAAC
TGAGAGAAGGAAAAGGAAACACAGTCTATTTGTGGGAGTTTCTTTTAGATCTACTTCAAGATAAACATACTTGTCCCCAG
TATATTAAATGGATCCAGAGAGAACAAGGCATATTCAAACTGGTGGATTCAAGGGCTGTCTCTAAGCTTTAGGAAAAGCA
TATGAACAAACCAAACGTGAACTGTGAAACTATGGAATGAGCTCTGAGATACTATTATCAAAGGGGAAATCTTGCAAAGC
CTGAAGGACAGAGGCTTGTATATCAGTTCAAGGATATGCCCCAATACATAGTGGTCATAGATGATGATAGAAATGAAACC
TGTAATGAAGATTTAGCAGGAGCTACTAATGAAAAATCATTAGATGAGTGCCACTGTCTACAGAAAGTCTCCTGAAAGCG
GCATCCTCTGTTTGTGGTGGCAAAATTCATCCCCTATAAACTTCTACAGGCAGAGAAGGGTGTAGCTGGAGTTGTGAATA
TCACTTCCCCTGGCCACGATGCTTCACCCAGGTTTCCAGCTACCACTGAGCCTATATCGGCAACAGCAGCTCCAAGGACA
GTTCATGTGGCAGTGCAGGTACTTGTTGAAATGACATTATTGGGTTAGAAGGCTTCAACTGTGGCAGTTCAGTCAGTTAA
TGTAGGTGCACCATTAATAACCAGCACTAGTCCAACAACAGTGACCTCTCCTAAGGCAGTCATTGAGATAAGCCTTACCA
TGATACCAGCTTCCACTGAAAACTGAAACAAAATCACCATACAGCCTGCCAAAATTATCACCATCCCAGCTACACGGCTT
GCACAGTGGTAACTGCAAACAAAGTCAGATTTGACTGGATCAGGAAGCATTAACATTGTTGCCATTCCCTTGGCTATGAG
AGCACTTACTCCC

Alignment

ORF - retro_cjac_540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.75 %
• Parental protein coverage: 59.36 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVSTEESEPMDTSPIPTSPDSHEPMKKKKVGRKPKTQQSPISNGSPELGIKKKPREGKGNTTYLWEFLLD
          E.STEESEP..TSPIPTSP.SHEPMKKKKVG...K.Q.SPIS.GSP.LGIK.K.REGKGNT.YLWEFLLD
Retrocopy EASTEESEPIHTSPIPTSPNSHEPMKKKKVGHEAKIQHSPISRGSPQLGIKRKLREGKGNTVYLWEFLLD

Parental  LLQDKNTCPRYIKWTQREKGIFKLVDSKAVSKLWGKHKNKPDMNYETMGRALRYYYQRGILAKVEGQRLV
          LLQDK.TCP.YIKW.QRE.GIFKLVDS.AVSKL..KH.NKP..N.ETM..ALRYYYQRG.LAK.EGQRLV
Retrocopy LLQDKHTCPQYIKWIQREQGIFKLVDSRAVSKL*EKHMNKPNVNCETME*ALRYYYQRGNLAKPEGQRLV

Parental  YQFKDMPKNIVVIDDDKSETCNEDLAGATDEKSLER-VSLSAESLLKAASSVRGGK-NSSSINCSR-AEK
          YQFKDMP..IVVIDDD..ETCNEDLAGAT.EKSL...V.LS.ESLLKAASSV.GGK.NSS.IN..R.AEK
Retrocopy YQFKDMPQYIVVIDDDRNETCNEDLAGATNEKSLDE<VPLSTESLLKAASSVCGGK<NSSPINFYR<AEK

Parental  GVARVVNITSSGHDASSRSPTTTASVSATAAPRTVRVAMQVPVVMTSLGQKISTVAVQSVNAGAPLITST
          GVA.VVNITS.GHDAS.R.P.TT...SATAAPRTV.VA.QV.V.MT.LG.K.STVAVQSVN.GAPLITST
Retrocopy GVAGVVNITSPGHDASPRFPATTEPISATAAPRTVHVAVQVLVEMTLLG*KASTVAVQSVNVGAPLITST

Parental  SPTTATSPKVVIQTIPTVMPASTENGDKITMQPAKIITIPATQLAQCQLQTKSNLTGSGSINIVGTPLAV
          SPTT.TSPK.VI....T..PASTEN..KIT.QPAKIITIPAT.LAQ..LQTKS.LTGSGSINIV..PLA.
Retrocopy SPTTVTSPKAVIEISLTMIPASTEN*NKITIQPAKIITIPATRLAQW*LQTKSDLTGSGSINIVAIPLAM

Parental  RALTP
          RALTP
Retrocopy RALTP

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	31.40 RPM
SRP051959_heart	0.00 RPM	38.62 RPM
SRP051959_kidney	0.00 RPM	35.76 RPM
SRP051959_liver	0.04 RPM	26.43 RPM
SRP051959_lung	0.00 RPM	49.10 RPM
SRP051959_lymph_node	0.00 RPM	52.97 RPM
SRP051959_skeletal_muscle	0.00 RPM	25.90 RPM
SRP051959_spleen	0.00 RPM	46.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_540 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_540 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003174	1 retrocopy	retro_cjac_540 ,
Homo sapiens	ENSG00000109381	1 retrocopy	retro_hsap_3546,
Macaca mulatta	ENSMMUG00000004984	1 retrocopy	retro_mmul_1813,
Pongo abelii	ENSPPYG00000015068	1 retrocopy	retro_pabe_2929,
Pan troglodytes	ENSPTRG00000016449	1 retrocopy	retro_ptro_2410,