RetrogeneDB ID: retro_cjac_3984

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286472.1:78864..79494(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SBDS
• Ensembl ID: ENSCJAG00000004283
• Aliases: None
• Description: Shwachman-Bodian-Diamond syndrome [Source:HGNC Symbol;Acc:19440]

Sequence

>retro_cjac_3984
AGTGGCATGGAAAAAGACCTTAATGAAGTTCCGCAGATGCACTCAGTGTTTGTAAATGTTTCTAAAGGTCAGGTTGCAAA
GAAGGAAGATCTCATCAGTGCATTTGGAACAGATGACCAAACTGAAAGCTGTAAGCAGATTTTGACTAAAGGAGAGGTTC
AAGTATCAGATAAAGAAAGACACACACGACTGGAGTAGATGTTTAGGGACATTGCAACTATTGTGGCAGACAAATGTATG
AATCCGGAAACAAAGAGACCATACACCGTGATCCTCATCGAGAGGGCCATGAAGTACATTCACTATTCAGTGAAAACCAA
CAAGAGTACCAAACAGCAGGTTTTGGAAGTAATAAAGCAGTTAAAAGAGAAAATGAAGATAGAGCGAGCTCACATGAGAC
TTCGGTTCATCCTTCCAGTGAATGAAGGGAAAAAGCTGAAAGAAAAACTCAAGCCACTGATCAAGGTCATAGAAAGTGAA
GATTATGGCCAACAGTTAGAAATCGTATGTCTTATTGACCCGGGTTGCTTCAGAGAAATCGATAAGCTAATAAAAAAGGA
AAGCAAAAGCAAAGGTTCTTTGGAAGTGCACAATTTCAAAGATGTGGAAGAAGGAGATGAGAAATTTGAA

Alignment

ORF - retro_cjac_3984 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.43 %
• Parental protein coverage: 84. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLITAFGTDDQTEICKQILTKGEVQVSDKERHTQLEQMFRD
          SG.EKDL.EV.Q.HSVFVNVSKGQVAKKEDLI.AFGTDDQTE.CKQILTKGEVQVSDKERHT.LE.MFRD
Retrocopy SGMEKDLNEVPQMHSVFVNVSKGQVAKKEDLISAFGTDDQTESCKQILTKGEVQVSDKERHTRLE*MFRD

Parental  IATIVADKCVNPETKRPYTVILIERAMKDIHYSVKTNKSTKQQALEVIKQLKEKMKIERAHMRLRFILPV
          IATIVADKC.NPETKRPYTVILIERAMK.IHYSVKTNKSTKQQ.LEVIKQLKEKMKIERAHMRLRFILPV
Retrocopy IATIVADKCMNPETKRPYTVILIERAMKYIHYSVKTNKSTKQQVLEVIKQLKEKMKIERAHMRLRFILPV

Parental  NEGKKLKEKLKPLIKVIESEDYGQQLEIVCLIDPGCFREVDELIKKETKGKGSLEVLSLKDVEEGDEKFE
          NEGKKLKEKLKPLIKVIESEDYGQQLEIVCLIDPGCFRE.D.LIKKE.K.KGSLEV...KDVEEGDEKFE
Retrocopy NEGKKLKEKLKPLIKVIESEDYGQQLEIVCLIDPGCFREIDKLIKKESKSKGSLEVHNFKDVEEGDEKFE

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	26.67 RPM
SRP051959_heart	0.00 RPM	29.85 RPM
SRP051959_kidney	0.04 RPM	29.60 RPM
SRP051959_liver	0.00 RPM	25.93 RPM
SRP051959_lung	0.00 RPM	37.71 RPM
SRP051959_lymph_node	0.00 RPM	18.45 RPM
SRP051959_skeletal_muscle	0.04 RPM	54.64 RPM
SRP051959_spleen	0.04 RPM	24.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3984 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3984 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3984 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003795	2 retrocopies	retro_chof_1999, retro_chof_623,
Callithrix jacchus	ENSCJAG00000004283	1 retrocopy	retro_cjac_3984 ,
Dasypus novemcinctus	ENSDNOG00000016904	1 retrocopy	retro_dnov_748,
Loxodonta africana	ENSLAFG00000008763	1 retrocopy	retro_lafr_920,
Monodelphis domestica	ENSMODG00000006644	1 retrocopy	retro_mdom_2004,
Mus musculus	ENSMUSG00000025337	1 retrocopy	retro_mmus_950,
Otolemur garnettii	ENSOGAG00000009011	1 retrocopy	retro_ogar_3368,
Ochotona princeps	ENSOPRG00000008721	6 retrocopies	retro_opri_1179, retro_opri_154, retro_opri_363, retro_opri_484, retro_opri_698, retro_opri_957,
Rattus norvegicus	ENSRNOG00000000888	1 retrocopy	retro_rnor_686,
Ictidomys tridecemlineatus	ENSSTOG00000022203	1 retrocopy	retro_itri_1763,