RetrogeneDB ID: retro_cjac_3866

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285402.1:2960..3612(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB11B
• Ensembl ID: ENSCJAG00000010778
• Aliases: None
• Description: RAB11B, member RAS oncogene family [Source:HGNC Symbol;Acc:9761]

Sequence

>retro_cjac_3866
ATGGGGACTGAGGACGACGAGTACGACTACCTATTCAAAGTGGTGCTTATTGGGGGACTCGGGCATGGGCAAGAGCAACC
TACTGTCCCACTTCACCCACAACGAGTTCAACCTGAAGAGCAAGAGCACCATTGGCATGGAGTTCACCACCCGCAGATTC
CACGTGGATGGAAAGACCATCAAGGCATAGATCTGGGACACCGCCAGCCAGGAGCGCTACTCCGCCATCACCTCTGCATA
CTATCGTGGCACTGCGGGCACCCTGCTGGTGTATTACACTGCCAAGCAACTGACCTATGAGAACGTGGAATACTCGCTGA
AGGAGCTTCAGGACCATGCAGACAGCAACATCGTCATCATGCTGGTGGGCAACAAAAGTGACCTGTGCCACCTGCGGGCT
GTGCCCACTGATGAGGCCTGTGCCTTCGCAGAAAAGAACAACTTGTCCTTCATTGAAACCTCAGCCTTGGATTCCATCAA
CATAGAGGAAGCCTTCAAGAACATTCTCTCAGAGATCTACCACATCATGTCACAGAAACAGATTGCAGACTGCGCAGCCC
ACAAGTCCCCTGGGAACAATGTGGTGGACATCAGCGTGCTGCTCATGACAGATGGATAGAAGCCCAAGAAGCTGCATTGC
TGCCAGAACCTG

Alignment

ORF - retro_cjac_3866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGTRDDEYDYLFKVVLIG-DSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAG
          MGT.DDEYDYLFKVVLIG.DSG.GKSNLLS.FT.NEFNL.SKSTIG.EF.TR...VDGKTIKA.IWDTA.
Retrocopy MGTEDDEYDYLFKVVLIG>DSGMGKSNLLSHFTHNEFNLKSKSTIGMEFTTRRFHVDGKTIKA*IWDTAS

Parental  QERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEA
          QERY.AITSAYYRG..G.LLVY..AK.LTYENVE..LKEL.DHADSNIVIMLVGNKSDL.HLRAVPTDEA
Retrocopy QERYSAITSAYYRGTAGTLLVYYTAKQLTYENVEYSLKELQDHADSNIVIMLVGNKSDLCHLRAVPTDEA

Parental  RAFAEKNNLSFIETSALDSTNVEEAFKNILTEIYHIMSQKQIADCAAHKSPGNNVVDISVLLTTDGQKPN
          .AFAEKNNLSFIETSALDS.N.EEAFKNIL.EIYHIMSQKQIADCAAHKSPGNNVVDISVLL.TDG.KP.
Retrocopy CAFAEKNNLSFIETSALDSINIEEAFKNILSEIYHIMSQKQIADCAAHKSPGNNVVDISVLLMTDG*KPK

Parental  KLHCCQNL
          KLHCCQNL
Retrocopy KLHCCQNL

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	1.86 RPM
SRP051959_heart	0.00 RPM	3.61 RPM
SRP051959_kidney	0.00 RPM	2.93 RPM
SRP051959_liver	0.00 RPM	1.75 RPM
SRP051959_lung	0.00 RPM	2.75 RPM
SRP051959_lymph_node	0.00 RPM	2.58 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.01 RPM
SRP051959_spleen	0.00 RPM	2.31 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3866 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3866 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3866 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013525	1 retrocopy	retro_chof_1582,
Callithrix jacchus	ENSCJAG00000007333	1 retrocopy	retro_cjac_1050,
Callithrix jacchus	ENSCJAG00000007715	1 retrocopy	retro_cjac_1256,
Callithrix jacchus	ENSCJAG00000010778	2 retrocopies	retro_cjac_3866 , retro_cjac_3917,
Erinaceus europaeus	ENSEEUG00000009165	2 retrocopies	retro_eeur_284, retro_eeur_565,
Mus musculus	ENSMUSG00000077450	1 retrocopy	retro_mmus_1846,
Otolemur garnettii	ENSOGAG00000003227	1 retrocopy	retro_ogar_2405,
Petromyzon marinus	ENSPMAG00000009335	1 retrocopy	retro_pmar_25,
Pteropus vampyrus	ENSPVAG00000009645	1 retrocopy	retro_pvam_64,
Tupaia belangeri	ENSTBEG00000000667	1 retrocopy	retro_tbel_4634,