RetrogeneDB ID: retro_cjac_399

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:59608853..59609580(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM66
• Ensembl ID: ENSCJAG00000012289
• Aliases: None
• Description: transmembrane protein 66 [Source:HGNC Symbol;Acc:28789]

Sequence

>retro_cjac_399
AAGACCGACTTAGATATTGCATACAAATTTGGGAATATTGTGGTGATCTGTGAAGGCTATGAGTCCTCTGAAGACCAGTA
TGTACCAAGAGGCTCCTGTGGTTTGGGGTATGATTTAGATTATGCGGAACTCGGCCTGCAGACACTGAAGGAGTCTGGAA
AGCAGCACGGTTGTGCCTCTTTCTCTGATTATTATTACAAGTGGTACTCGGCGGATTCCTGTAGCATGGGTGGATTAATT
ACCATCGTGATGCTCCTCAGGATTGCCTTTGTAGCTATAAGCTGTTCCGAGTGATCAGCAGTACTCTCCTCCACCGTATT
CTGAGTATCCTCCATTTCCCCACCGTTAACAGAGATTCACTAACTCAGCAGGACCTGTTCCCCGAGACTTTAAGTCTGAG
TTCACAGGACCGCAGAATACTGGCCCTGGTGCAACTTCTGGTTTTGGTAGTGCTTTTGCAGGGCAACGAGATTATGAAAA
TTCAGGACCAGGGTGCTGGACTGGCTTGGGAACAGGTGGAATATTAGGATATTTATGTGGCACCCATTGAGCGGCAACAC
CATTCTCAGACTCCTGGTACTACCCGTCCTATCCTCCCTCCTAATCTGGCACATAGAATAGTCGCGTTTACTCACCCCTT
TGTGGAGGCTCGGGTGACTCTTCAGCATGTTCAAACTCAAACATGAAAACCAGAACTGCATCAGAGTATGGTGGTCCCAG
GAGACGA

Alignment

ORF - retro_cjac_399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.78 %
• Parental protein coverage: 71.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KTDLDIAYKFGKTVVSCEGYESSEDQYVLRGSCGLEYNLDYTELGLKKLKESGKQHGFASFSDYYHKWYS
          KTDLDIAYKFG..VV.CEGYESSEDQYV.RGSCGL.Y.LDY.ELGL..LKESGKQHG.ASFSDYY.KWYS
Retrocopy KTDLDIAYKFGNIVVICEGYESSEDQYVPRGSCGLGYDLDYAELGLQTLKESGKQHGCASFSDYYYKWYS

Parental  ADSCNMSGLITIVVLLGIAFVV-YKLFL-SDGQYSPPSYSDYSTFSPRYQRFTNPSGPPPPGFKSEFTGP
          ADSC.M.GLITIV.LL.IAFV..YKLF..SD.QYSPP.YS.Y..F..R.QRFTN..GP.P..FKSEFTGP
Retrocopy ADSCSMGGLITIVMLLRIAFVA<YKLFR<SDQQYSPPPYSEYPPFPHR*QRFTNSAGPVPRDFKSEFTGP

Parental  QNTGRGATSGFGGAFAGQQGYENSGPGFWTGLGTGGLLGYLFGSNRAATPFSDSWYYPSYPPSYSGTWNS
          QNTG.GATSGFG.AFAGQ..YENSGPG.WTGLGTGG.LGYL.G...AATPFSDSWYYPSYPPS.SGT.NS
Retrocopy QNTGPGATSGFGSAFAGQRDYENSGPGCWTGLGTGGILGYLCGTH*AATPFSDSWYYPSYPPS*SGT*NS

Parental  RAYSPLRGGSGSYSACSNSDTKTRTASGYGGTRRR
          R.YSPL.GGSG..SACSNS..KTRTAS.YGG.RRR
Retrocopy RVYSPLCGGSGDSSACSNSNMKTRTASEYGGPRRR

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	65.36 RPM
SRP051959_heart	0.00 RPM	44.45 RPM
SRP051959_kidney	0.00 RPM	96.67 RPM
SRP051959_liver	0.00 RPM	82.14 RPM
SRP051959_lung	0.00 RPM	79.27 RPM
SRP051959_lymph_node	0.00 RPM	104.77 RPM
SRP051959_skeletal_muscle	0.00 RPM	50.99 RPM
SRP051959_spleen	0.00 RPM	142.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_399 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_399 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012289	1 retrocopy	retro_cjac_399 ,
Vicugna pacos	ENSVPAG00000004766	1 retrocopy	retro_vpac_375,