RetrogeneDB ID: retro_cjac_77

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01176946.1:24644..25214(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032493
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000032294
• Aliases: None
• Description: None

Sequence

>retro_cjac_77
ATGGCCTTGCCTTTTACTATATTGATGGCCCTAGTCATGCTCATCTGCAAGTCCATCTGCTCTCTGGGCTGTGATCTGCC
TCAGGCCCACAGCCTGAGTAACAGGAGGGCCTCCATACTCCTGGCACAAATGAGGAGAATCTCTCCTTTCTCTTGCCTGA
AGGACAGACAGGACTTTGTTTTCCCTCAAGAGGTGTTTTTTGGTGACCACTTCCAGAAGGCTCAAGCTATCTTCATCCTC
CATGAGATGATCCAGCAGACCTTCAACCTCTTTAGCACAAAGGACTCGTCCGTTACTTGGGATGCAACCCTTTTAGACAC
ATTTTACACTGAACTTTACAAGCAGCTGAATTACTTGGAAGCCTGTGTGATGCAGAGGATTGGAGTGGAAGGGACTCCCC
TGATGAATGCGGACTCTATCCTGGCTGTGAGGAAATACTTCGAAAGAATCACTCTCTATCTGACAGAAAAGAAACACAGC
CCTTGTGCCTGGGAGGTTGTCAGAGCAGAAATCATGAGATCCTTCTCTTTATTGACCAGCTTGCAAGAAAGATTAAGAAG
GAAGGAATGA

Alignment

ORF - retro_cjac_77 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALTFPLLMALMVLSYKSSCSLDCNLPQTHSLGNRRALVFLAQMRRISPFSCLKDRHDFGFPQKEFDGSQ
          MAL.F..LMAL..L..KS.CSL.C.LPQ.HSL.NRRA...LAQMRRISPFSCLKDR.DF.FPQ..F.G..
Retrocopy MALPFTILMALVMLICKSICSLGCDLPQAHSLSNRRASILLAQMRRISPFSCLKDRQDFVFPQEVFFGDH

Parental  LQKAQAIFVLHEMIQQNFNLFSTKDSSAAWDETLLEKFYTELYKQLNDLEACVMERIGVEGTPLMNADSI
          .QKAQAIF.LHEMIQQ.FNLFSTKDSS..WD.TLL..FYTELYKQLN.LEACVM.RIGVEGTPLMNADSI
Retrocopy FQKAQAIFILHEMIQQTFNLFSTKDSSVTWDATLLDTFYTELYKQLNYLEACVMQRIGVEGTPLMNADSI

Parental  LAVRKYFQRITLYLTEKKHSPCAWEVVRAEIMRSFSLLTSLQERLRRKE
          LAVRKYF.RITLYLTEKKHSPCAWEVVRAEIMRSFSLLTSLQERLRRKE
Retrocopy LAVRKYFERITLYLTEKKHSPCAWEVVRAEIMRSFSLLTSLQERLRRKE

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	0.04 RPM
SRP051959_heart	0.00 RPM	0.05 RPM
SRP051959_kidney	0.00 RPM	0.16 RPM
SRP051959_liver	0.00 RPM	0.15 RPM
SRP051959_lung	0.00 RPM	0.16 RPM
SRP051959_lymph_node	0.00 RPM	0.25 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_77 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_77 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_77 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032294	1 retrocopy	retro_cjac_77 ,