RetrogeneDB ID: retro_cjac_3990

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286608.1:4350..5753(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NONO
• Ensembl ID: ENSCJAG00000036744
• Aliases: None
• Description: None

Sequence

>retro_cjac_3990
ATGCAGAGTAATAAAACTTTTAACTTGGAGAAGCAAAATCATACTCCAAGAAAGCATCATCAACATCACCTCCAGCAGCA
GCACCCCAGCAGCAACAGCAACAGCTACCACCACCGCCAATACCTGCAAATGGGCAACAGGCCAGCAGCCAAAATGAAGG
CTTGACTATTGACCTGACGAATTTTAGGAAATCAGGACAGAAGACCTTCACCCAATGAAGCCATCTTTTTGTGGAAAATC
TTTCTCTCGACATCACTTAGGAAGAAATGAGGAAACTACTTGAGAAATATGGAAAGGCGTGTGAAGTCTTCATTCATAAG
GATCAAGGATTTGGCTTTATCCATTGGAAACACGAACCCTAGTAGAGACTGCCAAAGTGGAGCTGGACAATATGCCACTC
TGCGGAAAGCAGCTGCATGTTTCCTGCCATAGTGCATCCCTTACAGTTCGAAACCTTCCTCAGTATGTGTCCAACGAACT
GCTGGAAGACCCTTTTCTGTGTTTGGCAGGTGGAGATGGCTATAGTCATCATTGTGGATGATCGAGGAAGGCCCTCGGGA
AAAGGCATTGTTGAGTTCTCAGGGAAGCCAGCTGCTCGGAAAGCTCTGGACAGATGCAGTGAAAGCTCCTTCCTGCTAAT
CACATTTCCTCATCCTGAGACTGTGGAGCCCATGGACCAGTTAGAGGATGAAGAGCGACTTCTAGAGAAGCTGGTTATAA
AGAACCAGGATTTTAAAGGAACAAGAGCAGCCACCCAGATTTGCACAGCCTGGCTCCTTTGAATATGAGTATGCCATGTG
CCGGAAGGCACTCATTGAGATGGAGAAACAGCAGCAGGACCAAGTGGACCGCAACATCAAGGAGGCTCATGAAGCTGGAG
ATGGAGATAGAGATTGCATGCTTTGAACACCAGGTCATGCTAATGAGACAGGATTTGATGAGGCGCCAAGAAGAACTTCG
GAGGATGGAAGCACTGCCTAACCAACAGGTGCAAAAACGAAAGCAACTGGAGTTCAGGCAGGAGGAAGAGCACAGGCGCA
GTGGAGAAGAGATGCAGCGGCAGTAAGAAGAAATGATGCAACGACAGGAGGAAGGATTCAAGGGAACCTTCCTGGATGCG
AGACAGCAGGAGATTCGGATGGGTCAGATGGCTATGAGAGGTGCTATAGGTATAAACAACAGAGGTGCCATGCCCTCTAC
TCCTGTGGCATCTGGTACTCCAGCTCCTCCAGGACCTGCCCACTATGATGCCAGATGGGACCTTGAGACTGACCCCACCA
ACAACTGAACGCTTTGGTCAGGCTGCTACAATGGAAGGAATTGGGGCAATTGGCGGAACTCCTCCTGCATTCAACCATGC
AGCTCCCGGAGCTGATTTTGCTCCAAACAAACGTCGCTGATAC

Alignment

ORF - retro_cjac_3990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MQSNKTFNLEKQNHTPRKHHQHHHQQQHH-QQQQQQPPPPPIPANGQQASSQNEGLTIDLKNFRKPGEKT
          MQSNKTFNLEKQNHTPRKHHQHH.QQQH..QQQQQQ.PPPPIPANGQQASSQNEGLTIDL.NFRK.G.KT
Retrocopy MQSNKTFNLEKQNHTPRKHHQHHLQQQHP<QQQQQQLPPPPIPANGQQASSQNEGLTIDLTNFRKSGQKT

Parental  FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIR-LETRTLAEIAKVELDNMPLRGKQ
          FTQ.S.LFV.NL..DIT.EEMRKL.EKYGKA.EVFIHKD.GFGFI..LETRTL.E.AKVELDNMPL.GKQ
Retrocopy FTQ*SHLFVENLSLDIT*EEMRKLLEKYGKACEVFIHKDQGFGFIH<LETRTLVETAKVELDNMPLCGKQ

Parental  LRVRFACHSASLTVRNLPQYVSNELLEE-AFSVFG-QVERA-VVIVDDRGRPSGKGIVEFSGKPAARKAL
          L.V...CHSASLTVRNLPQYVSNELLE...FSVFG.QVE.A.V.IVDDRGRPSGKGIVEFSGKPAARKAL
Retrocopy LHV--SCHSASLTVRNLPQYVSNELLED<PFSVFG<QVEMAIVIIVDDRGRPSGKGIVEFSGKPAARKAL

Parental  DRCSEGSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQF-HKEREQPPRFAQPGSFEYEYAMRWKAL
          DRCSE.SFLL.TFP.P.TVEPMDQL.DEE.L.EKLVIKNQ.F.......P.RFAQPGSFEYEYAM..KAL
Retrocopy DRCSESSFLLITFPHPETVEPMDQLEDEERLLEKLVIKNQDF>KEQEQPP-RFAQPGSFEYEYAMCRKAL

Parental  IEMEKQQQDQVDRNIKEAREKLEMEME-AARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELR
          IEMEKQQQDQVDRNIKEA.E........A...............R..E.LRRME.L.NQ.VQKRKQLE.R
Retrocopy IEMEKQQQDQVDRNIKEAHEAGDGDRD>ACFEHQVMLMRQDLMRRQEE-LRRMEALPNQQVQKRKQLEFR

Parental  QEEERRRREEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAP
          QEEE.RR..EEM.RQ.EEMM.RQ.EGFKGTF.DAR.QEIRMGQMAM.GA.GINNRGAMP..PV..GTPAP
Retrocopy QEEEHRRSGEEMQRQ*EEMMQRQEEGFKGTFLDARQQEIRMGQMAMRGAIGINNRGAMPSTPVASGTPAP

Parental  PGPA-TMMPDGTLGLTPPTTERFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRRRY
          PGPA.TMMPDGTL.LTPPTTERFGQAATMEGIGAIGGTPPAFN.AAPGA.FAPNKRR.Y
Retrocopy PGPA>TMMPDGTLRLTPPTTERFGQAATMEGIGAIGGTPPAFNHAAPGADFAPNKRR*Y

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	0.02 RPM	45.26 RPM
SRP051959_heart	0.00 RPM	31.10 RPM
SRP051959_kidney	0.04 RPM	49.23 RPM
SRP051959_liver	0.06 RPM	43.65 RPM
SRP051959_lung	0.05 RPM	47.48 RPM
SRP051959_lymph_node	0.00 RPM	54.93 RPM
SRP051959_skeletal_muscle	0.02 RPM	24.15 RPM
SRP051959_spleen	0.04 RPM	50.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3990 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3990 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3990 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016057	2 retrocopies	retro_amel_1438, retro_amel_795,
Bos taurus	ENSBTAG00000012152	2 retrocopies	retro_btau_1027, retro_btau_313,
Canis familiaris	ENSCAFG00000017071	1 retrocopy	retro_cfam_98,
Callithrix jacchus	ENSCJAG00000001431	4 retrocopies	retro_cjac_1073, retro_cjac_2542, retro_cjac_2697, retro_cjac_486,
Callithrix jacchus	ENSCJAG00000036744	1 retrocopy	retro_cjac_3990 ,
Equus caballus	ENSECAG00000008502	2 retrocopies	retro_ecab_357, retro_ecab_427,
Felis catus	ENSFCAG00000014807	2 retrocopies	retro_fcat_1219, retro_fcat_147,
Homo sapiens	ENSG00000147140	1 retrocopy	retro_hsap_1699,
Gorilla gorilla	ENSGGOG00000006194	1 retrocopy	retro_ggor_1273,
Microcebus murinus	ENSMICG00000000232	1 retrocopy	retro_mmur_569,
Myotis lucifugus	ENSMLUG00000002489	1 retrocopy	retro_mluc_622,
Mustela putorius furo	ENSMPUG00000004937	1 retrocopy	retro_mputfur_937,
Mus musculus	ENSMUSG00000031311	2 retrocopies	retro_mmus_3652, retro_mmus_632,
Nomascus leucogenys	ENSNLEG00000001278	1 retrocopy	retro_nleu_1344,
Oryctolagus cuniculus	ENSOCUG00000021848	2 retrocopies	retro_ocun_1317, retro_ocun_1804,
Otolemur garnettii	ENSOGAG00000004834	3 retrocopies	retro_ogar_1525, retro_ogar_546, retro_ogar_593,
Pongo abelii	ENSPPYG00000020451	1 retrocopy	retro_pabe_1398,
Pan troglodytes	ENSPTRG00000022010	1 retrocopy	retro_ptro_1150,
Pteropus vampyrus	ENSPVAG00000016503	1 retrocopy	retro_pvam_444,
Rattus norvegicus	ENSRNOG00000003689	2 retrocopies	retro_rnor_1178, retro_rnor_1503,
Sorex araneus	ENSSARG00000007959	2 retrocopies	retro_sara_661, retro_sara_663,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,