RetrogeneDB ID: retro_cjac_3847

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285021.1:143480..143913(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000032468
• Aliases: None
• Description: None

Sequence

>retro_cjac_3847
ATGTTCCAGCAGATGCTCTAAGCCGTGCAGTACTGCCACAGAAAAAGAATAGCTCACAGAAACCTGAAACCAGACAACAT
CCTCTTGGACGGTGAAAGAAATATAAAAATTGCAGACTTTGGCTCAGCAACAACTTACCATGAGGGGCAGAGGCTGACAG
TATGTTGTGGCACCCTCCCCTACATGGCCCCAGAAGTCTTCCGGGTCAATGGGTAAATGTGCTATGGATATTTGGAGTTT
AGGCGTCACTTTGTTCGAGATGGTGTCTGTGACTCTGCCCTTCTTCTCAGAGAGTGCTGAGCCACTCAAATCCATAATTA
GATATGGAAAGTATGTTAGCCCTGACTACTTTTCAGAAGGCCTTAAAAGGCTAATGAAAAAACTGTTAATGTCAGACCCC
AAAAAGCGACCCACAGTAGAAGAAATTATGAGG

Alignment

ORF - retro_cjac_3847 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.46 %
• Parental protein coverage: 60.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFQQMLSAVRYLHRRSIAHRDLKPDNMLLDVKGNIKIADFGSATSYHEGQRLTIAHGTLAYMAPELF-GA
          MFQQML.AV.Y.HR..IAHR.LKPDN.LLD...NIKIADFGSAT.YHEGQRLT...GTL.YMAPE.F.G.
Retrocopy MFQQML*AVQYCHRKRIAHRNLKPDNILLDGERNIKIADFGSATTYHEGQRLTVCCGTLPYMAPEVF>GS

Parental  QGYECPAMDIWSLGVTLFQMVSNNLPFFAVSRTQLKRLIHRAPSSVPGGLSVFTLAVLWLCRSSPPCPQP
          .G..C.AMDIWSLGVTLF.MVS..LPFF..S...LK..I.......P...S............S.P...P
Retrocopy MG-KC-AMDIWSLGVTLFEMVSVTLPFFSESAEPLKSIIRYGKYVSPDYFSEGLKRLMKKLLMSDPKKRP

Parental  TLITLVK
          T......
Retrocopy TVEEIMR

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	0.44 RPM
SRP051959_heart	0.00 RPM	0.63 RPM
SRP051959_kidney	0.00 RPM	0.64 RPM
SRP051959_liver	0.04 RPM	0.37 RPM
SRP051959_lung	0.00 RPM	0.93 RPM
SRP051959_lymph_node	0.05 RPM	1.42 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.41 RPM
SRP051959_spleen	0.00 RPM	0.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3847 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3847 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3847 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032468	2 retrocopies	retro_cjac_1508, retro_cjac_3847 ,