RetrogeneDB ID: retro_cjac_2085

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:8878387..8878780(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBXN2A
• Ensembl ID: ENSCJAG00000007665
• Aliases: None
• Description: UBX domain protein 2A [Source:HGNC Symbol;Acc:27265]

Sequence

>retro_cjac_2085
CAACCTCTTGGTGATAATCAACAAACAAAGTGTGAATATCTTGTTAACAGCCTTTTTTATGAAGCTCAGAAGGTTGGTTC
CAAATGCTTGTCTCACACTGAACAGAAGAAACAGGTAGATATAAACATAAAAATTATGGGAAAATGGATTCACTGTCATG
ATGATTTCAGAAGTTATTCAAACGGGGCAAGTTAGCAATTTTTGAACTCCATCAAAAAGGGGGAATTACCCTAGAATTAC
AGGGAATTTTTGATAAAGAAGAGGTGGATGTTAAAGTTTAAGACAAGAAAAATAAAATATGCTATGAAGCCTGTCCTCCA
GCTCTTTTCAGGACAGGCTCACCAATCAGGAAGGGTAAGCCATATCAAAGACTTCACTGAAAAACACCAAGGA

Alignment

ORF - retro_cjac_2085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.99 %
• Parental protein coverage: 64.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QPLGNNQQSNCEYFVDSLFEEAQKVGSKCVSSTEQKKQVDVNIK-LWKNGFTV-NDDFRSYSDGASQQFL
          QPLG.NQQ..CEY.V.SLF.EAQKVGSKC.S.TEQKKQVD.NIK.LW.NGFTV..DDFRSYS.GAS.QFL
Retrocopy QPLGDNQQTKCEYLVNSLFYEAQKVGSKCLSHTEQKKQVDINIK>LWENGFTV<HDDFRSYSNGAS*QFL

Parental  NSIKKGELP-SELQRIFDKEEVD-VKVEDKKNEVCMSTKPVFQPFSGQGHRLGRVSHIKDFIEKYQG
          NSIKKGELP..ELQ.IFDKEEVD..K....K....M..KPV.Q.FSGQ.H..GRVSHIKDF.EK.QG
Retrocopy NSIKKGELP<LELQGIFDKEEVD>LKFKTRKIKYAM--KPVLQLFSGQAHQSGRVSHIKDFTEKHQG

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	0.49 RPM	6.66 RPM
SRP051959_heart	0.32 RPM	8.66 RPM
SRP051959_kidney	0.18 RPM	6.32 RPM
SRP051959_liver	0.06 RPM	2.23 RPM
SRP051959_lung	0.62 RPM	10.36 RPM
SRP051959_lymph_node	0.30 RPM	9.95 RPM
SRP051959_skeletal_muscle	0.04 RPM	15.77 RPM
SRP051959_spleen	0.53 RPM	6.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2085 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2085 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2085 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001640	5 retrocopies	retro_chof_1096, retro_chof_1171, retro_chof_2641, retro_chof_961, retro_chof_964,
Callithrix jacchus	ENSCJAG00000007665	1 retrocopy	retro_cjac_2085 ,
Equus caballus	ENSECAG00000020144	1 retrocopy	retro_ecab_569,
Echinops telfairi	ENSETEG00000002623	1 retrocopy	retro_etel_1116,
Homo sapiens	ENSG00000173960	1 retrocopy	retro_hsap_2025,
Gorilla gorilla	ENSGGOG00000002445	1 retrocopy	retro_ggor_1463,
Myotis lucifugus	ENSMLUG00000015640	1 retrocopy	retro_mluc_1195,
Macaca mulatta	ENSMMUG00000006487	1 retrocopy	retro_mmul_2068,
Mus musculus	ENSMUSG00000020634	1 retrocopy	retro_mmus_1007,
Nomascus leucogenys	ENSNLEG00000000751	1 retrocopy	retro_nleu_2612,
Oryctolagus cuniculus	ENSOCUG00000008783	1 retrocopy	retro_ocun_207,
Otolemur garnettii	ENSOGAG00000000025	1 retrocopy	retro_ogar_1909,
Procavia capensis	ENSPCAG00000011502	4 retrocopies	retro_pcap_169, retro_pcap_255, retro_pcap_271, retro_pcap_323,
Pan troglodytes	ENSPTRG00000011705	1 retrocopy	retro_ptro_1347,
Rattus norvegicus	ENSRNOG00000004950	2 retrocopies	retro_rnor_1746, retro_rnor_2966,
Sorex araneus	ENSSARG00000010108	1 retrocopy	retro_sara_272,
Sus scrofa	ENSSSCG00000026283	1 retrocopy	retro_sscr_537,
Tupaia belangeri	ENSTBEG00000012158	1 retrocopy	retro_tbel_3887,