RetrogeneDB ID: retro_cjac_4213

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:107934267..107935398(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000005017
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IFRD2
• Ensembl ID: ENSCJAG00000004993
• Aliases: None
• Description: interferon-related developmental regulator 2 [Source:HGNC Symbol;Acc:5457]

Sequence

>retro_cjac_4213
CCTGACCCCGCGCCCCCTGGGCGCCCCCCGTGCCGGGTTCCCAGCATGCCTCGCTCCCGTAAGGGCAACACGCTCCGAAA
GGGTGGTCAGCGCCGTGGAGGAGGTGCCCAGAGCAGTGCCCAAGCTGACTCAGGTTCCAGTGAGGATGAGGCAGCCAGTG
AGGCCCACAGCACCGCCAGTGAATGCCCCAGCCTTCTCAGCACCACTGCAGAGGACAGCCTTGGGGGGGATGTCGTGGAT
GAGCAGAGCCAGCAAGAAGACCTTGAGGAAAAGCTGAAGGAGTATGTGGACTGCCTCATAGACAAGAGTGCCAAGACCCG
GCAGGGTGCTCTTGAGAGCCTGCGCCTGGCCCTGGCGTCCCGCCTACTCCCCGACTTCTTGCTGGAGTGCCGCCTCACAC
TAGCCGATGCCCTGGAAAAGTGCCTCAAGAAAGGGAAGGGTGAGGAACAGGCCCTGGCGGCTCCTGTGCTAGGCCTGCTC
TGCGTGCAGCTGGGCCCTGGACCCAAGGGTGAGGAGCTGTTCCACAGCCTGCAGCCCCTGCTGGTCTCTGTGCTCAGTGA
CAGCACAGCTAGCCCTGCTGCCCAGCTCCACTGCGCTTCTTCTGCTCTTGGCCTGGGCTGCTGCGTGGCTGCCGCCGACA
TCCAGGACCTGGTCTCTTGCCTTGCCTGCTTAGAAAGTGTTTTCAGCCAGTTCTATGGCTTGGGTAGCTCTGCAACTCCT
GTGGTCCCTGCCAGCCTGCACGGCCTACTCTGTGCTGCCCTGCAGGCCTGGGCATTACTGCTCACCATCTGCCCCAGCAC
CCACTTCAGCCACATCCTTGACAGGCAGCTGCCCCGGCTGCCCCAGCTCTTGTCCAGTGAAAGTGTGAACCTGCGGATTG
CTGCCGGTGAAACCATTGCCCTGCTCTTTGAGCTTGCCCGGGACCTTGAGGAGGAGTTTGTTTACAAGGACATGGAGGCC
CTCTGCAGTGCCCTGCGCACTCTGGCCACTGACAGCAACAAGTACCGTGCCAAGGCCGATCGCCGGCGCCAGCGCTCTAC
TTTCTGCGCCGTGCTGCACTCCGTGGAGAACAATGAGCTACTCCGTGACATCTTTGGGCTGGGCCCTGTGCTGGTGCTGG
ATGCTGCTGCC

Alignment

ORF - retro_cjac_4213 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.06 %
• Parental protein coverage: 73.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRPLRPPRPPRPVPSMPRSRKGNTLRKGGQRRGGGAQSSAQADSGSSEDEAASEAHSTASECPSLLSTTA
          P.P..P.RPP..VPSMPRSRKGNTLRKGGQRRGGGAQSSAQADSGSSEDEAASEAHSTASECPSLLSTTA
Retrocopy PDPAPPGRPPCRVPSMPRSRKGNTLRKGGQRRGGGAQSSAQADSGSSEDEAASEAHSTASECPSLLSTTA

Parental  EDSLGGDVVDEQSQQEDLEEKLKEYVDCLTDKSAKTRQGALESLRLALASRLLPDFLLERRLTLADALEK
          EDSLGGDVVDEQSQQEDLEEKLKEYVDCL.DKSAKTRQGALESLRLALASRLLPDFLLE.RLTLADALEK
Retrocopy EDSLGGDVVDEQSQQEDLEEKLKEYVDCLIDKSAKTRQGALESLRLALASRLLPDFLLECRLTLADALEK

Parental  CLKKGKGEEQALAAAVLGLLCVQLGPGPKGEELFHSLQPLLVSVLSDSTASPAAQLHCA-SALGLGCYVA
          CLKKGKGEEQALAA.VLGLLCVQLGPGPKGEELFHSLQPLLVSVLSDSTASPAAQLHCA.SALGLGC.VA
Retrocopy CLKKGKGEEQALAAPVLGLLCVQLGPGPKGEELFHSLQPLLVSVLSDSTASPAAQLHCASSALGLGCCVA

Parental  AADIQDLVSCLACLESIFSQFYGLGSSATPVVPASLHGLLCAALQAWALLLTICPSTHFSHILDRQLPRL
          AADIQDLVSCLACLES.FSQFYGLGSSATPVVPASLHGLLCAALQAWALLLTICPSTHFSHILDRQLPRL
Retrocopy AADIQDLVSCLACLESVFSQFYGLGSSATPVVPASLHGLLCAALQAWALLLTICPSTHFSHILDRQLPRL

Parental  PQLLSSESVNLRIAAGETIALLFELARDLEEEFVYKDMEALCSVLRTLATDSNKYRAKADRRRQRSTFRA
          PQLLSSESVNLRIAAGETIALLFELARDLEEEFVYKDMEALCS.LRTLATDSNKYRAKADRRRQRSTF.A
Retrocopy PQLLSSESVNLRIAAGETIALLFELARDLEEEFVYKDMEALCSALRTLATDSNKYRAKADRRRQRSTFCA

Parental  VLHSVEGGECEEETVRFGFEVLYMDSWA
          VLHSVE..E........G..VL..D..A
Retrocopy VLHSVENNELLRDIFGLG-PVLVLDAAA

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	0.60 RPM	3.90 RPM
SRP051959_heart	0.12 RPM	4.98 RPM
SRP051959_kidney	0.13 RPM	3.26 RPM
SRP051959_liver	0.28 RPM	8.79 RPM
SRP051959_lung	0.37 RPM	3.90 RPM
SRP051959_lymph_node	0.30 RPM	4.31 RPM
SRP051959_skeletal_muscle	0.33 RPM	9.72 RPM
SRP051959_spleen	0.17 RPM	4.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4213 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4213 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4213 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004993	1 retrocopy	retro_cjac_4213 ,
Macaca mulatta	ENSMMUG00000020119	1 retrocopy	retro_mmul_1073,
Otolemur garnettii	ENSOGAG00000012534	1 retrocopy	retro_ogar_2236,
Sus scrofa	ENSSSCG00000024363	1 retrocopy	retro_sscr_445,