RetrogeneDB ID: retro_cjac_1006

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:114244522..114244889(+)
• Located in intron of: ENSCJAG00000012314

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1A
• Ensembl ID: ENSCJAG00000016353
• Aliases: None
• Description: SAR1 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:10534]

Sequence

>retro_cjac_1006
ATGTCTTTCATCTGTGAGTGGATCCACACTAGCTTCCACAGTGCACTCCAGTTCCTAGGACTCTACAAGAAATCTAGAAA
ACTTGTTCTCTTGGGTTGGGACAATGTGGATGAAACCATTTTTTCCTCACATGCTCAAAGACGGCCGATGGGGCCAAGAG
GCTGCAACACGACCTCTGACGTCAGCAGAGCTGACAACTCCTGGCATGACTTTTACAACTTCTGATCTTCTGAGGCATAA
GCAAGCACACTGGGTTTGGAACAGTGATCTCCCAGCAACAAATGGGATTGCCTTTCCAGGGGGCTGTGCAGATTGTCTTC
TGATCCTGGAATCCAAAGTGGAGCTCAACACTTTAATGACAGATAAA

Alignment

ORF - retro_cjac_1006 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.98 %
• Parental protein coverage: 61.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSFIFEWIYNGFSSVLQFLGLYKKSGKLVFLGLDNAGKTTLL-HMLKDDRLGQHVPTLHPTSEELTIAGM
          MSFI.EWI...F.S.LQFLGLYKKS.KLV.LG.DN...T....HMLKD.R.GQ...T...TS.ELT..GM
Retrocopy MSFICEWIHTSFHSALQFLGLYKKSRKLVLLGWDNVDETIFS>HMLKDGRWGQEAATRPLTSAELTTPGM

Parental  TFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADHSRLVESKVELNALMTDE
          TFTT.DL..H.QA..VW...LPA.NGI.F...CAD.....ESKVELN.LMTD.
Retrocopy TFTTSDLLRHKQAHWVWNSDLPATNGIAFPGGCADCLLILESKVELNTLMTDK

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	0.11 RPM	50.74 RPM
SRP051959_heart	0.04 RPM	50.20 RPM
SRP051959_kidney	0.09 RPM	69.71 RPM
SRP051959_liver	0.28 RPM	65.31 RPM
SRP051959_lung	0.16 RPM	58.29 RPM
SRP051959_lymph_node	0.30 RPM	43.93 RPM
SRP051959_skeletal_muscle	0.04 RPM	30.57 RPM
SRP051959_spleen	0.44 RPM	58.07 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1006 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1006 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1006 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_639
Pan troglodytes	retro_ptro_465
Pongo abelii	retro_pabe_565

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016353	5 retrocopies	retro_cjac_1006 , retro_cjac_2242, retro_cjac_2305, retro_cjac_4081, retro_cjac_957,
Homo sapiens	ENSG00000079332	4 retrocopies	retro_hsap_2976, retro_hsap_3568, retro_hsap_4714, retro_hsap_639,
Gorilla gorilla	ENSGGOG00000024879	3 retrocopies	retro_ggor_144, retro_ggor_2408, retro_ggor_2929,
Myotis lucifugus	ENSMLUG00000006626	2 retrocopies	retro_mluc_1317, retro_mluc_1996,
Nomascus leucogenys	ENSNLEG00000011243	4 retrocopies	retro_nleu_1987, retro_nleu_2231, retro_nleu_2311, retro_nleu_2759,
Otolemur garnettii	ENSOGAG00000005040	3 retrocopies	retro_ogar_1447, retro_ogar_1981, retro_ogar_2467,
Pongo abelii	ENSPPYG00000002374	4 retrocopies	retro_pabe_2468, retro_pabe_2940, retro_pabe_3661, retro_pabe_565,
Pan troglodytes	ENSPTRG00000002584	4 retrocopies	retro_ptro_2011, retro_ptro_2423, retro_ptro_3133, retro_ptro_465,
Ictidomys tridecemlineatus	ENSSTOG00000012780	2 retrocopies	retro_itri_1191, retro_itri_590,
Tupaia belangeri	ENSTBEG00000008657	5 retrocopies	retro_tbel_1060, retro_tbel_14, retro_tbel_2319, retro_tbel_2366, retro_tbel_2846,
Tarsius syrichta	ENSTSYG00000005955	2 retrocopies	retro_tsyr_1204, retro_tsyr_2099,
Vicugna pacos	ENSVPAG00000002631	2 retrocopies	retro_vpac_5, retro_vpac_77,