RetrogeneDB ID: retro_cjac_1321

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:13116169..13117858(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NLRP2
• Ensembl ID: ENSCJAG00000017689
• Aliases: None
• Description: None

Sequence

>retro_cjac_1321
CTTCCCAGCCACTGCCACAGCTACTGGGCAGGGATGGCAGCCATCCAGGTCCCTGAAAAGATGAACTAAACAGATTTTTC
TGAGAGAGCAAAGGATGAACTCAGAGAAGCAGCTTTGAAATCATATTATGAAAACAAGCCTCTATCATTTGGGATAATGT
GGACAGAAGAACCAAAATCCGTAGACCTGGAAGAAATACTGGAGCATTTTGAAGAGGAAGCACTAGAGTTTACAGAAATA
GAGAAAGATGTCATGAACCTGGGGGAAGCTAAAGAAGTCTTGCAAGGAGAAAAGCCAGGTAAAGAGGATAGTTACAGGAG
TATACTGTAGAAGAAGTGCCCGGAAGGGCTGGCCTGGAAACAGCAAAGGAGTCCACATTGTTGCCCAGAGATACAATATG
CTTATTCCATTCTGCAACCCCAAGGTGCTCCCAGGGCTGTTCCCCCCAGTAGTAGTGCTGCACGATCTTATGGGCTTTGG
GAAAATCACCCTTGCAAAGAAGTTAATGCTGGACTGGATGGAGGACAACCTCAGTCAGATATTCAAATAGGGTTTCTACT
TCAGCTGCAAGGAGCTCAGCCATGTGGGCCCCTGCAGTTTTGCAGACCTGGTTTTCAAGGACTGGCCTGATTTACAGGAT
TACACTCCAAACATCCTAGTCCAAGCACAGGAAATCCTGTTAGTTGTCGATGGCTTTGATGAGCTAAGAATCCCACCTGG
GGTGCTGATTCATAACATCTGCGGGGACTGGGAGAAGCAGAAGCCGGTGCCCATCCTCTTTGGGAGTTTGCTGAAGAGGA
AGATGGTACCCAAGGCCGCCCTGCTGGTCACCACGCAGCCTGGGACCCTGAGGGAGCTCTGGCTCCTGTTGGAGCATCCA
CTCTAAGTAAAGATGGAGGGGTTCCTGGAGCAGAACAGGAGGGGGTATTTCCTGAGATGATTTGGAGATGAGGACCAAGC
TCTGCAGCCTTTGAGCTGATGAGAAGCGACAGGGCCCTATTCCAGCTGGGTTCAGTGCATGTGGAGCACTGGGGGGTGTG
CAGGAGTCTGAAGCTGCAGATGGAGAAGGGGAAGGGCCTGGCTCCCCTCTGCCACACCTACATGGTACTGTTCCTGTGCT
TCCTCTGTGTCCAGTTTTCGCAGGGCGACCACCTTCAGGATGCTCTGCGGGCCCTGAGCCTCCTGGCTGTGCAGAACCTG
TGAGCACAGACATCTGTGTTTGATGGAAAACACCTGCATAGGCTCAGGGTGCAAGAGTCCAACCCCTGTAGTTTCCTGGA
AAGAGACATCCTTCGCCAGGACAGAGGCTCTGAAGGCTGCTACTCTTTCCTCCACCTCACCTTCCAGCAGTTTCTGGTAG
CATTATTCTATGTCCAGGAGAAGGAGGAGGAGGACAGGGACAGATTTGCCTGTATCATTGGCCTTGTGCAGCTGTATTCT
AGAGAAGAAAGACTCAAGAACCCCAACCTGATCCAAGCAGAACATTTCTTCTTTGGCCTCTCCAACAAGAAGAGAGCCAA
GGAGTTGGAAACCACTTTTGACTGCCAGATGTCACTGGAGATAAAACAAAAATTACTGAGATGTGATAAGGATAAACACT
CATCAGCTATGGACCTGAAGGAGCTCTTGTACTGCTTGTATGAATCTCAGGAGGAAGAGCTGGTGAAGGATATGATGGCA
CCAAAGAAA

Alignment

ORF - retro_cjac_1321 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.3 %
• Parental protein coverage: 71.61 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTSHCPSYWMETATIQVFEKMHRVDLSERVKDELREAALRSFNKNKPLPLETIRKGEPEPVDLDEMLVHF
          L.SHC.SYW...A.IQV.EKM...D.SER.KDELREAAL.S...NKPL........EP..VDL.E.L.HF
Retrocopy LPSHCHSYWAGMAAIQVPEKMN*TDFSERAKDELREAALKSYYENKPLSFGIMWTEEPKSVDLEEILEHF

Parental  KAEAQAFTETEEDVSSLREA-EALKKEMPGKEDRHRSIL-KMKFRQMWEAWPGASRGVQAVAQRYMTLIP
          ..EA..FTE.E.DV..L.EA.E.L..E.PGKED..RSIL.....R..W...PG.S.GV..VAQRY..LIP
Retrocopy EEEALEFTEIEKDVMNLGEAKEVLQGEKPGKEDSYRSIL>RRSARKGW---PGNSKGVHIVAQRYNMLIP

Parental  FSNPRILPGPFPHTVVLHGPAGLGKTTLAKRLMLDWTEDNLSHKFKYAFYLSCKRLSRLGLCSFAELVFR
          F.NP..LPG.FP..VVLH...G.GK.TLAK.LMLDW.EDNLS..FK..FY.SCK.LS..G.CSFA.LVF.
Retrocopy FCNPKVLPGLFPPVVVLHDLMGFGKITLAKKLMLDWMEDNLSQIFK*GFYFSCKELSHVGPCSFADLVFK

Parental  DWPELQGDVPDILAQAQKILFVVDGLDELGAPPGALIHDICGDWLKPKPVPVLLGSLLKRKMLPKAALLV
          DWP.LQ...P.IL.QAQ.IL.VVDG.DEL..PPG.LIH.ICGDW.K.KPVP.L.GSLLKRKM.PKAALLV
Retrocopy DWPDLQDYTPNILVQAQEILLVVDGFDELRIPPGVLIHNICGDWEKQKPVPILFGSLLKRKMVPKAALLV

Parental  TTRSWALRDLRPLMEQPIYIRVEGFLEEDRRAYFLTHFGEEDQA-TRAFELMRSNAALFQLGSAPAVCWM
          TT....LR.L..L.E.P.....EGFLE..RR.YFL..FG.EDQA...AFELMRS..ALFQLGS.....W.
Retrocopy TTQPGTLRELWLLLEHPL*VKMEGFLEQNRRGYFLR*FGDEDQA<SAAFELMRSDRALFQLGSVHVEHWG

Parental  VCTSLKLQMENGEDPATTCHTRTGLFLHFLCSRFPKGAQLGGTLRALSILAAQGLWAQMSVFHREDLESF
          VC.SLKLQME.G...A..CHT...LFL.FLC..F..G..L...LRALS.LA.Q.L.AQ.SVF....L...
Retrocopy VCRSLKLQMEKGKGLAPLCHTYMVLFLCFLCVQFSQGDHLQDALRALSLLAVQNL*AQTSVFDGKHLHRL

Parental  RVQESDLRPFLDRGILRQDRDSKDCYSFLHLSFQQFFTALFYALEKEEEDRDGHAWDIGDVQRLLSGEER
          RVQES....FL.R.ILRQDR.S..CYSFLHL.FQQF..ALFY..EKEEEDRD..A..IG.VQ.L.S.EER
Retrocopy RVQESNPCSFLERDILRQDRGSEGCYSFLHLTFQQFLVALFYVQEKEEEDRDRFACIIGLVQ-LYSREER

Parental  VQNPDLIQAGHFLFGLANEKRAAELETTFGCVMSREIKQELLRCDIICEEDRYSTLTDLKEVLHCLYESQ
          ..NP.LIQA.HF.FGL.N.KRA.ELETTF.C.MS.EIKQ.LLRCD.....D..S...DLKE.L.CLYESQ
Retrocopy LKNPNLIQAEHFFFGLSNKKRAKELETTFDCQMSLEIKQKLLRCD----KDKHSSAMDLKELLYCLYESQ

Parental  EGELVKAVMAPLK
          E.ELVK..MAP.K
Retrocopy EEELVKDMMAPKK

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	0.02 RPM
SRP051959_heart	0.18 RPM	0.00 RPM
SRP051959_kidney	0.11 RPM	0.00 RPM
SRP051959_liver	0.54 RPM	0.00 RPM
SRP051959_lung	0.34 RPM	0.00 RPM
SRP051959_lymph_node	0.21 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.00 RPM
SRP051959_spleen	0.17 RPM	0.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1321 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1321 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1321 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017689	2 retrocopies	retro_cjac_1321 , retro_cjac_3184,
Myotis lucifugus	ENSMLUG00000015486	1 retrocopy	retro_mluc_1353,
Pan troglodytes	ENSPTRG00000011480	1 retrocopy	retro_ptro_3224,