RetrogeneDB ID: retro_cjac_1037

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:50718090..50718446(-)
• Located in intron of: ENSCJAG00000007538

Retrocopy information

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

Parental gene information

• Parental gene symbol: HCFC1R1
• Ensembl ID: ENSCJAG00000015444
• Aliases: None
• Description: host cell factor C1 regulator 1 (XPO1 dependent) [Source:HGNC Symbol;Acc:21198]

Sequence

>retro_cjac_1037
ATGATCCTGGAGCAGGCCTTGGAGCGAGGCCCGCAGGGTGGGGCCCAGCGCTTCCCGCGGGCCGCCTTGGGGGTGACTCG
CGGCCTGGACGCTAGGGAGCCTCTGCGCAAGCAGTTTTTGTCTGAGGAGAACATGGCCACCCATTTCTCTCAACTCAGCC
TGCACAATGATCACCCCTACTGCAGCCCCCCATGACCTTCCCCCCGGCCCTGACCCCACTCAGGAGCTCTTGCTCTGAGC
TGCTTCTCTGGCGATACCCTGGCAGCCTGATCCCTGCAGCCCTCCGGCTGCTGAGGCTGGGGGACATCCCCAGTCCCTCC
TACCCCTCGACCCCAGCTGGGGACATAATGGAGCTC

Alignment

ORF - retro_cjac_1037 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MILEQPLERGPQGGAQRLPRAALGVTRGLDAREPLRKQFLSEENMATHFSQLSLHNDHPYCSPP-MTFPP
          MILEQ.LERGPQGGAQR.PRAALGVTRGLDAREPLRKQFLSEENMATHFSQLSLHNDHPYCSPP.MTFPP
Retrocopy MILEQALERGPQGGAQRFPRAALGVTRGLDAREPLRKQFLSEENMATHFSQLSLHNDHPYCSPP<MTFPP

Parental  ALPPLRSSCSELLLWRYPGSLIPEALRLLRLGDIPSPSYPSTPAGDIMEL
          AL.PLRSSCSELLLWRYPGSLIP.ALRLLRLGDIPSPSYPSTPAGDIMEL
Retrocopy ALTPLRSSCSELLLWRYPGSLIPAALRLLRLGDIPSPSYPSTPAGDIMEL

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	0.04 RPM	4.15 RPM
SRP051959_heart	0.04 RPM	13.28 RPM
SRP051959_kidney	0.00 RPM	12.49 RPM
SRP051959_liver	0.02 RPM	2.23 RPM
SRP051959_lung	0.02 RPM	5.29 RPM
SRP051959_lymph_node	0.05 RPM	2.79 RPM
SRP051959_skeletal_muscle	0.02 RPM	30.35 RPM
SRP051959_spleen	0.02 RPM	2.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1037 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1037 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1037 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005504	1 retrocopy	retro_amel_1251,
Callithrix jacchus	ENSCJAG00000015444	1 retrocopy	retro_cjac_1037 ,
Mus musculus	ENSMUSG00000023904	5 retrocopies	retro_mmus_1485, retro_mmus_1577, retro_mmus_1646, retro_mmus_2644, retro_mmus_767,