RetrogeneDB ID: retro_cjac_2473

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:126024828..126025521(-)
• Located in intron of: ENSCJAG00000003719

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPF2
• Ensembl ID: ENSCJAG00000005212
• Aliases: None
• Description: ribosome production factor 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20870]

Sequence

>retro_cjac_2473
CAGACATCACTGGAATTCTTTTCAAAGAAGTCAGACTGTTCTTTATTTATGTTTGGCTCCCATAATAAGAAGCAGCCAAA
TAATCTAGTCATAGGTCGTATGTATGACTACCATGTGCTAGATATGATTGAATTAGGTATTGAGAATTTTGTCTCTCTAA
AAGACATTAAGAACAGTAAATGCCCTGAGGGAACAAAACCCATGTGAATATTTGCTGGTGATGATTTTGATGTAACAGAA
GATTATAGAAGACTAAAAAGTCTTCTTATTGATTTCTTCAGAGGCCCCACAGTATCAAATATCCACCTGGCTGGATTAGA
GTATGTTCTGCACTTTACTGCACTGAATGGGATGCACTTTCGAAGCTATAAGCTGCTGCTGAAGAAATCTGGTTGCTGAA
CACCATGAACTGAATTAGAAGAAATGGACCCTCACATTGGATCTGGTTCTGAGGAGGGCACACCTGGCATCGGATGACCT
TTATAAATTATCTATGAAATTCCAAAAGCTCTCAAGCCAAAGAAGAAGAAAAATATCTCCCATGATACTTTTGGTACAAC
TTATGGAAGTATTCATATGCAGAAGCAAGACCTAAGCAAACTACAAACCAGGAAAATAATGGGGTTGAAGAAGCGACCTG
CAGAAAGGATAACAGAAGACCAGGAGAAAAAGTAAAAAAGAATTTTAAAAAAT

Alignment

ORF - retro_cjac_2473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.03 %
• Parental protein coverage: 75.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QTSLEFFSKKSDCSLFMFGSHNKKRPNNLVIGRMYDYHVLDMIELGIENFVSLKDIKNSKCPEGTKPMLI
          QTSLEFFSKKSDCSLFMFGSHNKK.PNNLVIGRMYDYHVLDMIELGIENFVSLKDIKNSKCPEGTKPM.I
Retrocopy QTSLEFFSKKSDCSLFMFGSHNKKQPNNLVIGRMYDYHVLDMIELGIENFVSLKDIKNSKCPEGTKPM*I

Parental  FAGDDFDVTEDYRRLKSLLIDFFRGPAVSNIRLAGLEYVLHFTALNGKIYFRSYKLLLKKSGCRTPRIEL
          FAGDDFDVTEDYRRLKSLLIDFFRGP.VSNI.LAGLEYVLHFTALNG...FRSYKLLLKKSGC.TP..EL
Retrocopy FAGDDFDVTEDYRRLKSLLIDFFRGPTVSNIHLAGLEYVLHFTALNG-MHFRSYKLLLKKSGC*TP*TEL

Parental  EEMGP-SLDLVLRRTHLASDDLYKLSMK-MPKALKPKKKKNISHDTFGTTYGRIHMQKQDLSKLQTRKMK
          EEM.P..LDLVLRR.HLASDDLYKLSMK..PKALKPKKKKNISHDTFGTTYG.IHMQKQDLSKLQTRK..
Retrocopy EEMDP>TLDLVLRRAHLASDDLYKLSMK<IPKALKPKKKKNISHDTFGTTYGSIHMQKQDLSKLQTRKIM

Parental  GLKKRPAERITEDQEKKSKRIKKN
          GLKKRPAERITEDQEKK.KRI.KN
Retrocopy GLKKRPAERITEDQEKK*KRILKN

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	0.80 RPM	3.53 RPM
SRP051959_heart	0.58 RPM	5.49 RPM
SRP051959_kidney	2.48 RPM	6.90 RPM
SRP051959_liver	0.37 RPM	4.96 RPM
SRP051959_lung	0.80 RPM	4.38 RPM
SRP051959_lymph_node	1.35 RPM	5.37 RPM
SRP051959_skeletal_muscle	0.04 RPM	7.34 RPM
SRP051959_spleen	1.58 RPM	5.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2473 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2473 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2473 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003918	2 retrocopies	retro_cfam_1611, retro_cfam_903,
Callithrix jacchus	ENSCJAG00000005212	6 retrocopies	retro_cjac_1675, retro_cjac_1768, retro_cjac_2244, retro_cjac_2473 , retro_cjac_606, retro_cjac_933,
Cavia porcellus	ENSCPOG00000006797	2 retrocopies	retro_cpor_332, retro_cpor_582,
Equus caballus	ENSECAG00000017121	1 retrocopy	retro_ecab_782,
Erinaceus europaeus	ENSEEUG00000006169	2 retrocopies	retro_eeur_454, retro_eeur_584,
Felis catus	ENSFCAG00000001527	1 retrocopy	retro_fcat_1584,
Homo sapiens	ENSG00000197498	1 retrocopy	retro_hsap_2425,
Gorilla gorilla	ENSGGOG00000001469	1 retrocopy	retro_ggor_83,
Myotis lucifugus	ENSMLUG00000005676	2 retrocopies	retro_mluc_485, retro_mluc_921,
Macaca mulatta	ENSMMUG00000021532	1 retrocopy	retro_mmul_1903,
Mus musculus	ENSMUSG00000038510	1 retrocopy	retro_mmus_2234,
Nomascus leucogenys	ENSNLEG00000012854	3 retrocopies	retro_nleu_2024, retro_nleu_2434, retro_nleu_2445,
Oryctolagus cuniculus	ENSOCUG00000016028	1 retrocopy	retro_ocun_831,
Pongo abelii	ENSPPYG00000016925	2 retrocopies	retro_pabe_1788, retro_pabe_2464,
Pan troglodytes	ENSPTRG00000018503	1 retrocopy	retro_ptro_1398,
Rattus norvegicus	ENSRNOG00000000587	1 retrocopy	retro_rnor_2336,
Tupaia belangeri	ENSTBEG00000017151	9 retrocopies	retro_tbel_1824, retro_tbel_2243, retro_tbel_2376, retro_tbel_2576, retro_tbel_3547, retro_tbel_3635, retro_tbel_3803, retro_tbel_3876, retro_tbel_4509,