RetrogeneDB ID: retro_cjac_707

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:82966943..82967405(+)
• Located in intron of: ENSCJAG00000018672

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCGF3
• Ensembl ID: ENSCJAG00000001960
• Aliases: None
• Description: polycomb group ring finger 3 [Source:HGNC Symbol;Acc:10066]

Sequence

>retro_cjac_707
ATGTAGACCAGAAGGATGAAGCTGTGGGACAGTAATGCCCACATCACCTGCTGCCTGTGTACTGGGCACCTCACTGATGC
AACCAGGGTGGCCAAGTGTCTGCACATATTCTGTAAGCATTGCCTGGTCAAGTATTTGGAAGAGAACGACACCTACCCTT
CCTATAGGACTGTGATGCATCACAGCTACGCACTCTGGTACATCAGTCATGACAGCACCATACATGGGATTGTTTATCAA
TCAGTATCAGGTCTCCAGGAGCAGAAATGAAAACAGAGAAAGAATTCTGCCACAAATTGGGCATGGAAGTGCCTGAAGAC
ATCAAGGGGGAGAATTGTTCCACCAAACAACACTTAGATTTTCATCAGAATGGTGAAATGAAAGCAGAAGACAGTTAAAC
AGAGACCAGAAAAAAAGAAGGAAAAGGACAAAGATTTTCACAGAAGTGATGAGCAGGAAAGC

Alignment

ORF - retro_cjac_707 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.0 %
• Parental protein coverage: 64.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLTRKIKLWDINAHITCRLCSGYLIDATTVTECLHTFCRSCLVKYLEENNTCPTCRIVIHQSHPLQYIGH
          M.TR..KLWD.NAHITC.LC.G.L.DAT.V..CLH.FC..CLVKYLEEN.T.P..R.V.H.S..L.YI.H
Retrocopy M*TRRMKLWDSNAHITCCLCTGHLTDATRVAKCLHIFCKHCLVKYLEENDTYPSYRTVMHHSYALWYISH

Parental  DRTMQDIVYKLVPGLQE-AEMRKQREFYHKLGMEVPGDIKGETCSAKQHLDSHRNGKGETKADDS-SNKE
          D.T...IVY..V.GLQE.AEM....EF.HKLGMEVP.DIKGE.CS.KQHLD.H.N..GE.KA.DS.....
Retrocopy DSTIHGIVYQSVSGLQE<AEMKTEKEFCHKLGMEVPEDIKGENCSTKQHLDFHQN--GEMKAEDS>KQRP

Parental  AAEEKPEEDNDYHRSDEQVS
          ........D...HRSDEQ.S
Retrocopy EKKKEKDKD--FHRSDEQES

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	4.68 RPM
SRP051959_heart	0.00 RPM	4.79 RPM
SRP051959_kidney	0.00 RPM	5.70 RPM
SRP051959_liver	0.00 RPM	2.36 RPM
SRP051959_lung	0.00 RPM	5.56 RPM
SRP051959_lymph_node	0.00 RPM	6.10 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.61 RPM
SRP051959_spleen	0.00 RPM	4.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_707 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_707 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_707 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001960	1 retrocopy	retro_cjac_707 ,
Callithrix jacchus	ENSCJAG00000011001	1 retrocopy	retro_cjac_2702,
Callithrix jacchus	ENSCJAG00000036548	1 retrocopy	retro_cjac_2437,
Macaca mulatta	ENSMMUG00000012624	1 retrocopy	retro_mmul_2182,
Monodelphis domestica	ENSMODG00000005677	3 retrocopies	retro_mdom_1481, retro_mdom_885, retro_mdom_985,
Nomascus leucogenys	ENSNLEG00000000926	1 retrocopy	retro_nleu_1826,
Otolemur garnettii	ENSOGAG00000015569	1 retrocopy	retro_ogar_2846,