RetrogeneDB ID: retro_cjac_4136

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:6868749..6870125(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOLC1
• Ensembl ID: ENSCJAG00000017832
• Aliases: None
• Description: nucleolar and coiled-body phosphoprotein 1 [Source:HGNC Symbol;Acc:15608]

Sequence

>retro_cjac_4136
GCCATCTCCAAGAAGACTGTACCTTAAAGGAAAGCTGTGACCAAGATTCCAGTGAAAGCAGCTGCCAGCCCTATCCGAAA
GAGTTCCAGCAGTGAGGACCCCTCCAGTGAGGAGTAAGAGGAGTAGGAAAAAAGAATCATGAAAAAAAAAAAAAAAAAAC
AGGTCTCTAAAGTTCAGTTTCCCCTGCATGCTCCCCCATCAAAGAAGTCCTTGGGAACCCAGCCTCCCAAGAAAGCTGTG
GAGAAGGAAAAGCCTTCCAAAAGCAGCGATGAATCTGTTTCAAGTTTGCAGGAAGAGGAGAAACTCTGGCTAATGCAATC
ATCTCTAAAGCAACCACTAAACAACTTCCAGCAAAGAAAGCAGCAGAGAGCTCTTCAGACAGCTCTGAGACTCCAACAGC
TCTGAGGATGATGAAGTTCCTTCCAAGCCAGCCAGTACCAGCAAGAATTCCTCAAATAAGCCAGCTGCCACTACCAAGTC
ACGTGCAGTGGAGCCAGCTGCAACCCTCAAGCAACCAGTAAGCAGTGGCCAGAAGCCTCTGATGAGGAAGGCTGACAGTG
GCTCCAGTGAGGAAGAGAGCAGTTCCAGTGAGGAGGAGAAGACAAAGACGACTGTGGCCACTCCTAAGCCCAAGGTGACT
GACAAAGTAGCTCCATATCTGCCTGCCAAGCAGGCTCCTGAGGGTGGTAAGGACAGCAACTTTGATTCATACAGCTCTAG
CAGTGAAGAGGAGAAAGAGAAGACAGCTAAACCCCCAGTTAAAAAGAAGTTGAGGAAGCCAGCAGGAGGCACAGTCCTTT
CCAAGCCAGCCTCCACAAAGAAAGGAAAGGCCGAGAGCAGCCGCAGTTCTTCCTCTGATAACTCCAGTGAGGAGGAGGAA
GAGAAACCCAAAGGCAAGGGCTCTCCAAAATCACAAGTCCCCAGGACCAATGGCACCTCTGCTCTGACTTCCCACAATGG
AAAAGCACCTAAGAATAGTGAAGAGGAGGAAGAAGAAAAGAAAAAGGCAGCAGTGGCAGTTTCCAAGCTGAGTTCAGGAA
AGAAATGGATGCAGAATGAGGCTGCCACGGAGGCATATACTCCGCAAACCAAGAAGATAAAACTTCAGACACCTAACACA
TTTCCAAAAAGGAAGAAAGGAGGAAAAAAGGTATGATCCCCATCCTGAAGGGTCAGGGAGGAAGAAATTGAGGTGGCAGA
CAACTCCTTTGATGCCAACAACTGAGGTGCAGCCGGACAGAGGGAAACCAGCCAATCAAGCTTTGAAGTTCACCAAAGTC
AAATCCTTCTGGCGTGAGAAAACCAAGAAGAAGTAGGGCAGCTACTGGGCAGGCTCGATCTCTGTCCAGGTCAATTCTTT
AAAGTTTGACAGCAAG

Alignment

ORF - retro_cjac_4136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.44 %
• Parental protein coverage: 65.59 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVGEETVPKKQVVAKAPVKAAATPTQKSSSSEDSSSEE-EEQQKKPMKN-KPGPYSSVP-PPSAPPPKKT
          .....TVP....V.K.PVKAAA.P..KSSSSED.SSEE.EE..K..MK..K....S.V..P..APP.KK.
Retrocopy AISKKTVP*RKAVTKIPVKAAASPIRKSSSSEDPSSEE*EE*EKRIMKKKKKKQVSKVQFPLHAPPSKKS

Parental  LGTQPPKKAVEKQQPVESSEDSSDESDSSSEEEKK-SPAKAVVSKATTKPPPAKKAAES-SSDSS-DSDS
          LGTQPPKKAVEK..P......SSDES.SS..EE.K...A.A..SKATTK..PAKKAAES.S..S..DS.S
Retrocopy LGTQPPKKAVEKEKPSK----SSDESVSSLQEEEK<TLANAIISKATTKQLPAKKAAESSSDSSE<DSNS

Parental  SEEDEDPSKPAGTTKNSSHKPAGTTKSPAAKPAAAPKQSLGGGQKPLMRKADSSSSEEESSSSEEEKTKK
          SE.DE.PSKPA.T.KNSS.KPA.TTKS.A..PAA..KQ....GQKPLMRKADS.SSEEESSSSEEEKTK.
Retrocopy SEDDEVPSKPASTSKNSSNKPAATTKSRAVEPAATLKQPVSSGQKPLMRKADSGSSEEESSSSEEEKTKT

Parental  TVATTKPKATAKAAPPLPAKQAPQGSRDSSSDSDSSSSEEEEEEKTSKTAVKKKPQEVAGGAAPSKPASA
          TVAT.KPK.T.K.AP.LPAKQAP.G..DS..DS.SSSS.EEE.EKT.K..VKKK....AGG...SKPAS.
Retrocopy TVATPKPKVTDKVAPYLPAKQAPEGGKDSNFDSYSSSS-EEEKEKTAKPPVKKKLRKPAGGTVLSKPAST

Parental  KKGKPESSSSSSSDDSSEEEEEKPKGKGKGTPRPQALKASSTSALTAQNGKAAKNS-EEEEEKKKAAVAV
          KKGK.ESS.SSSSD.SSEEEEEKP..KGKG.P..Q......TSALT..NGKA.KNS.EEEEEKKKAAVAV
Retrocopy KKGKAESSRSSSSDNSSEEEEEKP--KGKGSPKSQVPRTNGTSALTSHNGKAPKNSEEEEEEKKKAAVAV

Parental  SKPGSLKKRKQNEAAKEAETPQAKKIKLQTPNTFPKRKKGEKRASSPFRRVREEEIEVDSRVADNSFDAK
          SK..S.KK..QNEAA.EA.TPQ.KKIKLQTPNTFPKRKKG.K...SP..RVREEEIEV....ADNSFDA.
Retrocopy SKLSSGKKWMQNEAATEAYTPQTKKIKLQTPNTFPKRKKGGKKV*SPS*RVREEEIEV----ADNSFDAN

Parental  RGAAG-DWGERANQVLKFTKGKSFRHEKTKKKRGSYRGGSISVQVNSVKFDSE
          ...A..D.G..ANQ.LKFTK.KSF..EKTKKK.GSY..GSISVQVNS.KFDS.
Retrocopy N*GAA>DRGKPANQALKFTKVKSFWREKTKKK*GSYWAGSISVQVNSLKFDSK

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	0.00 RPM	25.47 RPM
SRP051959_heart	0.39 RPM	24.78 RPM
SRP051959_kidney	0.00 RPM	26.91 RPM
SRP051959_liver	0.00 RPM	32.21 RPM
SRP051959_lung	0.00 RPM	29.56 RPM
SRP051959_lymph_node	0.00 RPM	33.90 RPM
SRP051959_skeletal_muscle	0.00 RPM	31.36 RPM
SRP051959_spleen	0.00 RPM	29.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4136 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4136 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010062	1 retrocopy	retro_cfam_1047,
Callithrix jacchus	ENSCJAG00000017832	2 retrocopies	retro_cjac_4136 , retro_cjac_4187,
Homo sapiens	ENSG00000166197	1 retrocopy	retro_hsap_4781,
Nomascus leucogenys	ENSNLEG00000015012	1 retrocopy	retro_nleu_1101,
Pongo abelii	ENSPPYG00000002595	1 retrocopy	retro_pabe_3721,
Pan troglodytes	ENSPTRG00000023882	1 retrocopy	retro_ptro_3182,
Tursiops truncatus	ENSTTRG00000014974	1 retrocopy	retro_ttru_155,