RetrogeneDB ID: retro_cjac_432

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:81545536..81546140(+)
• Located in intron of: ENSCJAG00000004536

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM17
• Ensembl ID: ENSCJAG00000020573
• Aliases: None
• Description: None

Sequence

>retro_cjac_432
GATTATGATCCTATGTTTCCTAATGACTATGAGAAATTAGTGAAACACCAACTTCACTACAGCGAACGGCAGACACAGCA
GGAGCTCGAAATACGAAAGGAAATAGAAGAAAGGGAAAAGAGGCCTAAAGCCAGGCAAGAAGCTAGGAGGGTTCTGATCA
AGGCGACCATATCCAGATTCTGATGAAGACGAAGATTAGGAGCGAGAGAGGAGGAAAAGAAATAGAGCGGAGCTGCCATT
GCCCGCCCACTTCTCTCGTAGACAAGGAGTCACCCAGAGGTTTTCCTGATGAAGAGGATTCAAGACCTTAATCACGGTCT
TCCAAAGCTGCCTTTCCTCCCCCAGTGAAGCTGGAACAGGACAGAGCAAGATCTCCAAATCGGCCTAGCACCTCCTTCCT
CGCTAAAGGCGTGGGAACTGTGGCGCACAACATCATGCAGAAGCCCGGCTTCCGGGAAGGCCAGGGCCTAGGGGAGCACC
AGCAGGGGCTGCGCACCACGTTTCCGGTGGAAAAGACCGGTAAGCCTGGCAGCAACATCATCATGGACTAGGCCCCAGAG
AAAGACGCTTTCAAGAATCAGGTACAAATCCACTGACAGAAATA

Alignment

ORF - retro_cjac_432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.71 %
• Parental protein coverage: 50.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EYDPMFPNDYEKVVKRQRE--ERQRQRELERQKEIEEREKRRKDRHEA-SGF-SRRPDPDSDEDEDYERE
          .YDPMFPNDYEK.VK.Q....ERQ.Q.ELE..KEIEEREKR.K.R.EA..GF.SRRP.PDSDEDED.ERE
Retrocopy DYDPMFPNDYEKLVKHQLHYSERQTQQELEIRKEIEEREKRPKARQEA>GGF*SRRPYPDSDEDED*ERE

Parental  RRKRSMG-GAAIA-PPTSLVEKDKELPRDFPYEEDSRPRSQSSKAAIPPPMYEEQDRPRSPTGPSNSFLA
          RRKR....GAAIA.PPTSLV..DKE.PR.FP.EEDSRP.S.SSKAA.PPP...EQDR.RSP..PS.SFLA
Retrocopy RRKRNRA<GAAIA<PPTSLV--DKESPRGFPDEEDSRP*SRSSKAAFPPPVKLEQDRARSPNRPSTSFLA

Parental  NMGGTVAHKIMQKYGFREGQGLGKHEQGLSTALSVEKTSKRGGKIIVGDATEKDASK-KSDSNPLTEI
          ...GTVAH.IMQK.GFREGQGLG.H.QGL.T...VEKT.K.G..II...A.EKDA.K..S..NPLTEI
Retrocopy KGVGTVAHNIMQKPGFREGQGLGEHQQGLRTTFPVEKTGKPGSNIIMD*APEKDAFK<ESGTNPLTEI

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	18.55 RPM
SRP051959_heart	0.05 RPM	20.86 RPM
SRP051959_kidney	0.00 RPM	25.54 RPM
SRP051959_liver	0.00 RPM	18.63 RPM
SRP051959_lung	0.00 RPM	24.81 RPM
SRP051959_lymph_node	0.00 RPM	23.31 RPM
SRP051959_skeletal_muscle	0.00 RPM	19.83 RPM
SRP051959_spleen	0.02 RPM	23.36 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_432 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_432 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_432 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021951	2 retrocopies	retro_btau_1057, retro_btau_530,
Canis familiaris	ENSCAFG00000005206	1 retrocopy	retro_cfam_844,
Callithrix jacchus	ENSCJAG00000020573	1 retrocopy	retro_cjac_432 ,
Equus caballus	ENSECAG00000008939	1 retrocopy	retro_ecab_547,
Erinaceus europaeus	ENSEEUG00000013077	1 retrocopy	retro_eeur_390,
Homo sapiens	ENSG00000134453	1 retrocopy	retro_hsap_1551,
Macropus eugenii	ENSMEUG00000011347	1 retrocopy	retro_meug_438,
Macaca mulatta	ENSMMUG00000015152	2 retrocopies	retro_mmul_1209, retro_mmul_771,
Mus musculus	ENSMUSG00000037197	1 retrocopy	retro_mmus_2855,
Otolemur garnettii	ENSOGAG00000015687	1 retrocopy	retro_ogar_1119,
Pongo abelii	ENSPPYG00000002067	1 retrocopy	retro_pabe_1284,
Pan troglodytes	ENSPTRG00000002265	1 retrocopy	retro_ptro_1044,
Ictidomys tridecemlineatus	ENSSTOG00000013591	1 retrocopy	retro_itri_1376,
Tursiops truncatus	ENSTTRG00000001344	1 retrocopy	retro_ttru_1758,