RetrogeneDB ID: retro_cjac_1059

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:97827403..97827961(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023002
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SSR3
• Ensembl ID: ENSCJAG00000004643
• Aliases: None
• Description: signal sequence receptor, gamma (translocon-associated protein gamma) [Source:HGNC Symbol;Acc:11325]

Sequence

>retro_cjac_1059
ATGGCTCCCAAAGGCAGTTCCAAACAGCAGTCCGAGGAGGACCTGCTCCTGCAGGATTTCAGCCGCAACGTCTCAGCCAA
GTCCTCCGCGCTCTTCTTCGGGAACGCTTTCATCGTGTCTGCCTTCCCCATCTGGTTATACTGGAGAATACCGCATATGG
ATCTTACTCAGTCTGCTGTTTTGTATAGTGTGATGACTCTAGTAAGCACATATTTGGTAGCCTTTGCATACGGGAATGTG
AAATTTGTTCTCAAGCCCAAAGTGGCACAGAAGAGGGAGGATGCTGTTTCCAAAGAAATGACTCGAAAACTTTCTGAAGC
TGATAATAGAAAGATGTCTCGGAAGGAGAAAGATGAAAGAATCTTGTGGAAGAAGAATGAAGTTGCTGATTATGAAGCTA
CAACATTTTCCATCTTCTATAACAGCACTCTGTTGTTCGTGGTCTTGGTCACTGTTGCTTCCTTCTTCATACTGAGGAAC
TTCAACCCCACAGTGAACTACATTTTGTCCATAAGTGCTTCATCAGGACTTATCGCCCTCCTGTCTACTGGCTCCAAG

Alignment

ORF - retro_cjac_1059 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPKGSSKQQSEEDLLLQDFSRNLSAKSSALFFGNAFIVSAIPIWLYWRIWHMDLIQSAVLYSVMTLVST
          MAPKGSSKQQSEEDLLLQDFSRN.SAKSSALFFGNAFIVSA.PIWLYWRI.HMDL.QSAVLYSVMTLVST
Retrocopy MAPKGSSKQQSEEDLLLQDFSRNVSAKSSALFFGNAFIVSAFPIWLYWRIPHMDLTQSAVLYSVMTLVST

Parental  YLVAFAYKNVKFVLKHKVAQKREDAVSKEVTRKLSEADNRKMSRKEKDERILWKKNEVADYEATTFSIFY
          YLVAFAY.NVKFVLK.KVAQKREDAVSKE.TRKLSEADNRKMSRKEKDERILWKKNEVADYEATTFSIFY
Retrocopy YLVAFAYGNVKFVLKPKVAQKREDAVSKEMTRKLSEADNRKMSRKEKDERILWKKNEVADYEATTFSIFY

Parental  NNT-LFLVLVIVASFFILKNFNPTVNYILSISASSGLIALLSTGSK
          N.T.LF.VLV.VASFFIL.NFNPTVNYILSISASSGLIALLSTGSK
Retrocopy NSTLLFVVLVTVASFFILRNFNPTVNYILSISASSGLIALLSTGSK

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	0.11 RPM	58.38 RPM
SRP051959_heart	0.04 RPM	46.50 RPM
SRP051959_kidney	0.04 RPM	49.48 RPM
SRP051959_liver	0.06 RPM	89.78 RPM
SRP051959_lung	0.05 RPM	38.10 RPM
SRP051959_lymph_node	0.02 RPM	46.87 RPM
SRP051959_skeletal_muscle	0.00 RPM	51.91 RPM
SRP051959_spleen	0.04 RPM	56.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1059 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1059 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1059 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003125	1 retrocopy	retro_amel_832,
Canis familiaris	ENSCAFG00000008870	5 retrocopies	retro_cfam_1296, retro_cfam_1370, retro_cfam_1924, retro_cfam_2029, retro_cfam_2041,
Choloepus hoffmanni	ENSCHOG00000001517	1 retrocopy	retro_chof_29,
Callithrix jacchus	ENSCJAG00000004643	4 retrocopies	retro_cjac_1059 , retro_cjac_1503, retro_cjac_2369, retro_cjac_3213,
Cavia porcellus	ENSCPOG00000005898	2 retrocopies	retro_cpor_1243, retro_cpor_826,
Dasypus novemcinctus	ENSDNOG00000000752	2 retrocopies	retro_dnov_1922, retro_dnov_632,
Homo sapiens	ENSG00000114850	1 retrocopy	retro_hsap_173,
Gorilla gorilla	ENSGGOG00000024038	1 retrocopy	retro_ggor_255,
Myotis lucifugus	ENSMLUG00000015478	3 retrocopies	retro_mluc_1624, retro_mluc_1728, retro_mluc_2146,
Macaca mulatta	ENSMMUG00000016970	1 retrocopy	retro_mmul_383,
Otolemur garnettii	ENSOGAG00000010589	2 retrocopies	retro_ogar_2089, retro_ogar_3483,
Pongo abelii	ENSPPYG00000014233	1 retrocopy	retro_pabe_456,
Pan troglodytes	ENSPTRG00000015560	1 retrocopy	retro_ptro_163,
Tarsius syrichta	ENSTSYG00000010578	1 retrocopy	retro_tsyr_660,