RetrogeneDB ID: retro_cjac_1420

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:82903647..82904433(-)
• Located in intron of: ENSCJAG00000009359

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS26A
• Ensembl ID: ENSCJAG00000012907
• Aliases: None
• Description: None

Sequence

>retro_cjac_1420
ATGAGTTTTCTTGGAGGCTTTTTGGGTCCAATTTGTGAGATCCATATTATCTTTAATGATGGGGAAGCCAGGAAAATGAC
AGAAATGAAAACTGAAGATGGCAAAGTAGAAAAACACTATCTCTTTATGATAGAGAATCTGTTTCAGGTAAGGTAAACCT
AGCCTTTAAGCAACCTGGATAGAGGCTAGAGCACCAAGGAATCAGAATTGAATTTGTAGGTCAAATGGAACTTTTCAATG
ACAAGAGTAATGCTCATGAATTTATAAACCTAGTGAAAGAACTAGCCTTACCTGGAGAACTGACTCAGACAAGAAGTTAT
GCTTTTGAATTTATGCAAGTTGAAAAGCCATATGAATCTTACATCGGTGCCAATGTCCACTTGTTATTTTCTTAAAGTGA
CAATAGTAAGAAGACTGACAGATTTAGCGAAAGAATATGATCTTACTGTTCATCAGCTTGCCACCTGTCCTGATGTTAAC
AACTGTATTAAGATGGCAGTGGGCACTGAAGATTGTCTACACATATAATTTGAATATAATAAATCAAAATATCATTTAAA
GCATGTACTTGTTTGAAAATTTTACTTTGTAGTAGTAAGAATAAAAATACAACATATGGAGTTGCAATTGATCAAAAAAG
AGATCACAGGAATTGGACCCAGTCCCACAGCAGAAACAGAAACAATCACCGAATATGAAGTCATGGACGGTGCACCAGTA
GAAGGTGAATCGATTCCAATGAGACTACTTTTAGTGGAATATGACCCACGTCCAACAATGAAAAAT

Alignment

ORF - retro_cjac_1420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.08 %
• Parental protein coverage: 80.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSFLGGFFGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLF-YDGESVSGKVNLAFKQPGKRLEHQGIR
          MSFLGGF.GPICEI.I..NDGE.RKM.EMKTEDGKVEKHYLF.YD.ESVSGKVNLAFKQPG.RLEHQGIR
Retrocopy MSFLGGFLGPICEIHIIFNDGEARKMTEMKTEDGKVEKHYLF<YDRESVSGKVNLAFKQPG*RLEHQGIR

Parental  IEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRY-FL-KVTIV
          IEFVGQ.ELFNDKSN.HEF.NLVKELALPGELTQ.RSY.FEFMQVEKPYESYIGANV.L...FL.KVTIV
Retrocopy IEFVGQMELFNDKSNAHEFINLVKELALPGELTQTRSYAFEFMQVEKPYESYIGANVHLLF<FL<KVTIV

Parental  RRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHM
          RRLTDL.KEYDL.VHQLAT.PDVNN.IKM.VG.EDCLHI.FEYNKSKYHLK.V.V.K.YF..VRIKIQHM
Retrocopy RRLTDLAKEYDLTVHQLATCPDVNNCIKMAVGTEDCLHI*FEYNKSKYHLKHVLV*KFYFVVVRIKIQHM

Parental  ELQLIKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRD
          ELQLIKKEITGIGPS.T.ETETI..YE.MDGAPV.GESIP.RL.L..YDP.PTM..
Retrocopy ELQLIKKEITGIGPSPTAETETITEYEVMDGAPVEGESIPMRLLLVEYDPRPTMKN

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	1.51 RPM	11.25 RPM
SRP051959_heart	0.23 RPM	11.70 RPM
SRP051959_kidney	1.22 RPM	12.96 RPM
SRP051959_liver	1.84 RPM	6.15 RPM
SRP051959_lung	0.65 RPM	13.49 RPM
SRP051959_lymph_node	0.16 RPM	9.06 RPM
SRP051959_skeletal_muscle	0.04 RPM	8.25 RPM
SRP051959_spleen	0.29 RPM	11.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1420 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1420 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1420 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013827	1 retrocopy	retro_cfam_1133,
Choloepus hoffmanni	ENSCHOG00000007324	5 retrocopies	retro_chof_1303, retro_chof_1663, retro_chof_1796, retro_chof_2352, retro_chof_242,
Callithrix jacchus	ENSCJAG00000012907	1 retrocopy	retro_cjac_1420 ,
Equus caballus	ENSECAG00000009507	1 retrocopy	retro_ecab_17,
Homo sapiens	ENSG00000122958	1 retrocopy	retro_hsap_2688,
Gorilla gorilla	ENSGGOG00000010433	1 retrocopy	retro_ggor_1875,
Microcebus murinus	ENSMICG00000014940	1 retrocopy	retro_mmur_1070,
Mustela putorius furo	ENSMPUG00000004519	1 retrocopy	retro_mputfur_146,
Nomascus leucogenys	ENSNLEG00000011548	1 retrocopy	retro_nleu_1187,
Pongo abelii	ENSPPYG00000002386	1 retrocopy	retro_pabe_2293,
Pan troglodytes	ENSPTRG00000002567	3 retrocopies	retro_ptro_1815, retro_ptro_2245, retro_ptro_4,
Tupaia belangeri	ENSTBEG00000015348	1 retrocopy	retro_tbel_1425,
Vicugna pacos	ENSVPAG00000000630	1 retrocopy	retro_vpac_385,