RetrogeneDB ID: retro_cjac_2182

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:125024912..125025720(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF38
• Ensembl ID: ENSCJAG00000010299
• Aliases: None
• Description: None

Sequence

>retro_cjac_2182
CCTCCAATGCTTCAGGCATGTTCAGTTCAGCACTTACCAGTACCATATGCTGCATTCCCACCCCGTATTTCTAGTGATCC
ATTTCTTATACATCTTCCTCACCTTTCTCCCCATCATACGCGTTTGCCACCACCAGGCCAGTTTGTCCCTTTCCAAACAC
AGCAATCATGATTGCCTCTGCAAAAGATAGAAAATGAAGTGGAACTCTTAGGAAAACATCTTCCAGTAGGAAGTTTTACT
TACCCTCCATCAGCCCACCCCCAACATTACCTCCATCAGCTCCTTTGCAGTTCTTAACACAAGATCCTTTGCATCAGGAG
CTGTCCTTTGGAGTACCTTACCATCCATTTGTGCCTCGGAAGCTCACAAGATGTAGTAGCTGTCCATCCTAGCAGCCAAT
ATTACCTCCCCTTATCATCCCAGCTTACTGCCATATGCGTTATCAATGCTTCCAGTGCCACCTGCAGTGGGTCCAACTTT
CAACTTTCAATTAGATGTAGAAGATGAAGAAGTAGAAAATTATGAGGCACTGTTCAACCTGGCAGAGTGACTGGGAGAGG
CAAAGCTTTGTGGACTGACTAAAGCTGTTAATGAACAACTTCCTTCTTATCGGCTCAATCCTAACAACCACCAGTCAGAA
CAGACTTTGTGTGTAGTATGCATGTGTGATTTTGAGTCAAGGCAGCTATTTAGAGTCTTACCCTGTAACCACTAGCTCCA
TGCCAAGTGTGTTGACAAATGACTTAAGGCAAATTGTACTTATCCAATATGCAGAGCTGATGCTTCAGAAGTGCATCGGG
ATTCAGAA

Alignment

ORF - retro_cjac_2182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 58.28 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPMLQACSVQHLPVPYAAFPPLISSDPFLIHPPHLSPHHPPHLPPPGQFVPFQTQQSRSPLQRIENEVEL
          PPMLQACSVQHLPVPYAAFPP.ISSDPFLIH.PHLSPHH...LPPPGQFVPFQTQQS..PLQ.IENEVEL
Retrocopy PPMLQACSVQHLPVPYAAFPPRISSDPFLIHLPHLSPHHT-RLPPPGQFVPFQTQQS*LPLQKIENEVEL

Parental  LGEHLPVGGFTYPPSAHPA-TLPPSAPLQFLTHDPLHQEVSFGVPYPPFMPRRLTGRSRYRSQQPIPPP-
          LG.HLPVG.FTYPPSAHP..TLPPSAPLQFLT.DPLHQE.SFGVPY.PF.PR.LT..S...S.QPI.PP.
Retrocopy LGKHLPVGSFTYPPSAHPQ<TLPPSAPLQFLTQDPLHQELSFGVPYHPFVPRKLTRCSSCPS*QPILPP<

Parental  PYHPSLLPYVLSMLPVPPAVGPTFSFELDVEDGEVENYEALLNLAERLGEAKPRGLTKADIEQLPSYRFN
          PYHPSLLPY.LSMLPVPPAVGPTF.F.LDVED.EVENYEAL.NLAE.LGEAK..GLTKA..EQLPSYR.N
Retrocopy PYHPSLLPYALSMLPVPPAVGPTFNFQLDVEDEEVENYEALFNLAE*LGEAKLCGLTKAVNEQLPSYRLN

Parental  PNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADASEVHRDSE
          PNNHQSEQTLCVVCMCDFESRQL.RVLPCNH..HAKCVDK.LKAN.T.PICRADASEVHRDSE
Retrocopy PNNHQSEQTLCVVCMCDFESRQLFRVLPCNH*LHAKCVDK*LKANCTYPICRADASEVHRDSE

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	0.04 RPM	10.69 RPM
SRP051959_heart	0.00 RPM	9.82 RPM
SRP051959_kidney	0.02 RPM	12.62 RPM
SRP051959_liver	0.00 RPM	4.64 RPM
SRP051959_lung	0.00 RPM	17.08 RPM
SRP051959_lymph_node	0.00 RPM	12.76 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.35 RPM
SRP051959_spleen	0.00 RPM	12.54 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2182 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2182 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2182 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005519	1 retrocopy	retro_btau_396,
Callithrix jacchus	ENSCJAG00000010299	1 retrocopy	retro_cjac_2182 ,
Monodelphis domestica	ENSMODG00000002665	1 retrocopy	retro_mdom_1075,