RetrogeneDB ID: retro_cjac_610

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:126740189..126740636(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000034702
• Aliases: None
• Description: None

Sequence

>retro_cjac_610
AAATTCAGTTCATGCTCGACAATTTTTCTTGAAGACAGCACAGCCAGCTGCCCTGATTTTGAAACGACACTACACTATGT
CGCCTTGGAGTTGTATTTTCTTATCAAGGAAAGAAAAGGAAATATATCTTTCACAATATTTGATGAACGTGTATACCCAT
TGGAAGACGAAATGGAAAAATACATTATGTGTGATCCTTCACAGACAATGATTTACGAATTTATACATTCCCTGTTTTAT
GTAAAAATTCTAAATGTTGCTGATGTCATCAAAAGTAGGGTGTATATCCAAAGACTTGTGCACTGTGCTTCTATGTACAT
TCGTCCAACCACCTGGAGGAGGATTATCCTCGGAGCCTTTCTTCTTGTCATCAAGGTTGGGAGCAATGTGGCTGTGTGCA
ATGAGGACTTATGCATGCGCTTTGAGAAAACTACAGTTGACGATCTG

Alignment

ORF - retro_cjac_610 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.13 %
• Parental protein coverage: 62.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KFSSCSTIFLEDSTASCPHFETTLKSVALDFYFLIKDREGYLSYKIFDEHAYPLKYRTEEYIMYDPSETM
          KFSSCSTIFLEDSTASCP.FETTL..VAL..YFLIK.R.G..S..IFDE..YPL....E.YIM.DPS.TM
Retrocopy KFSSCSTIFLEDSTASCPDFETTLHYVALELYFLIKERKGNISFTIFDERVYPLEDEMEKYIMCDPSQTM

Parental  IYKFIRTLFYVKSLKVAVAIIIMVYIQRLIRYSRIYICSATWRRIILGAILVAIKVRSNVPVCNKDLCRR
          IY.FI..LFYVK.L.VA..I...VYIQRL......YI...TWRRIILGA.L..IKV.SNV.VCN.DLC.R
Retrocopy IYEFIHSLFYVKILNVADVIKSRVYIQRLVHCASMYIRPTTWRRIILGAFLLVIKVGSNVAVCNEDLCMR

Parental  FEKTTVDDL
          FEKTTVDDL
Retrocopy FEKTTVDDL

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	4.13 RPM	3.46 RPM
SRP051959_heart	5.00 RPM	5.19 RPM
SRP051959_kidney	8.16 RPM	6.59 RPM
SRP051959_liver	5.42 RPM	6.30 RPM
SRP051959_lung	10.15 RPM	5.21 RPM
SRP051959_lymph_node	8.97 RPM	7.17 RPM
SRP051959_skeletal_muscle	2.97 RPM	2.58 RPM
SRP051959_spleen	7.84 RPM	6.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_610 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_610 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_610 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001008	1 retrocopy	retro_cjac_3555,
Callithrix jacchus	ENSCJAG00000002901	1 retrocopy	retro_cjac_569,
Callithrix jacchus	ENSCJAG00000011445	1 retrocopy	retro_cjac_1164,
Callithrix jacchus	ENSCJAG00000034702	1 retrocopy	retro_cjac_610 ,
Homo sapiens	ENSG00000163249	3 retrocopies	retro_hsap_1629, retro_hsap_1984, retro_hsap_4845,
Mus musculus	ENSMUSG00000070871	1 retrocopy	retro_mmus_3072,