RetrogeneDB ID: retro_cjac_978

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:48643557..48644001(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPA17
• Ensembl ID: ENSCJAG00000007961
• Aliases: None
• Description: sperm autoantigenic protein 17 [Source:HGNC Symbol;Acc:11210]

Sequence

>retro_cjac_978
ATGTCCGTTCCATTCTCCAACACCCACTACTGATTCCGTAAGGATTTGGGAGTCTTCCTGAAGGGGTGACCCATGAGATT
CTGAGAGAGCAGCTAGATAACATACAGCTTTTGCAGCAGCATATTTTGAGAGCTTTCTAGAGAAAAGAGAGAAAAACCAC
CTTTGATCCAGCAGAATGGGGCTCAGGGACAAGACCGCCTCTACAGCAATCACGCATTGGAGGATCAAGAACCACCTGAT
AAATGTGATCCTAAACAAGAAAAGTCTCCGATACCTGGGGAGGAGGAAGAGACACCAGTCACCATCTTAGACTCTTCTGG
GGAAGATAGGGAAAGAGAAGAGGTTTCTGCTGTTAAAATCCAAGCTCCCTTCCAGGGACATACAGCCAGAGAGGAGGTAA
AGAGAATGGAAACAGTCTCCAACATGAAGACAGAGGAAAACAAG

Alignment

ORF - retro_cjac_978 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.79 %
• Parental protein coverage: 96.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSIPFSNTH-CRIPQGFGNLLEGLTREILREQPDNIP-AFAAAYFQSLLEKREKTNFDPAEWG-SKIDDR
          MS.PFSNTH...IP.GFG.L.EG.T.EILREQ.DNI..AFAAAYF.S.LEKREK........G.....DR
Retrocopy MSVPFSNTH<LLIP*GFGSLPEGVTHEILREQLDNIQ<AFAAAYFESFLEKREKNHL*SSRMG<AQGQDR

Parental  FYNNHAFEKQEPPEKCDPKQEKSQISGKEEETPVTILDSSEEDKEKEEVAAVKIQAAFRGHIAREEVKKM
          .Y.NHA.E.QEPP.KCDPKQEKS.I.G.EEETPVTILDSS.ED.E.EEV.AVKIQA.F.GH.AREEVK.M
Retrocopy LYSNHALEDQEPPDKCDPKQEKSPIPGEEEETPVTILDSSGEDREREEVSAVKIQAPFQGHTAREEVKRM

Parental  KTDSLQNEEDEE
          .T.S....E...
Retrocopy ETVSNMKTEENK

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	0.02 RPM
SRP051959_heart	0.18 RPM	0.21 RPM
SRP051959_kidney	0.11 RPM	0.60 RPM
SRP051959_liver	0.06 RPM	0.04 RPM
SRP051959_lung	0.13 RPM	1.59 RPM
SRP051959_lymph_node	0.00 RPM	0.14 RPM
SRP051959_skeletal_muscle	0.04 RPM	0.13 RPM
SRP051959_spleen	0.27 RPM	0.23 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_978 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_978 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_978 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_696
Pan troglodytes	retro_ptro_500
Gorilla gorilla	retro_ggor_593
Pongo abelii	retro_pabe_529
Macaca mulatta	retro_mmul_2405

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007961	1 retrocopy	retro_cjac_978 ,
Echinops telfairi	ENSETEG00000007789	1 retrocopy	retro_etel_911,
Homo sapiens	ENSG00000064199	1 retrocopy	retro_hsap_696,
Gorilla gorilla	ENSGGOG00000003757	1 retrocopy	retro_ggor_593,
Macaca mulatta	ENSMMUG00000008480	1 retrocopy	retro_mmul_2405,
Nomascus leucogenys	ENSNLEG00000007436	1 retrocopy	retro_nleu_2229,
Pongo abelii	ENSPPYG00000004017	1 retrocopy	retro_pabe_529,
Pan troglodytes	ENSPTRG00000004426	1 retrocopy	retro_ptro_500,
Tarsius syrichta	ENSTSYG00000008379	1 retrocopy	retro_tsyr_2091,