RetrogeneDB ID: retro_cjac_3184

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:15496134..15498197(+)
• Located in intron of: ENSCJAG00000001570

Retrocopy information

• Ensembl ID: ENSCJAG00000001581
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_3184
GAGACAATACGGAAAGGAGAACCGAAGCCTGTAGACCTGGATGAAATGCTGGTGCGCTTAGAGACAGAAGCACAAGCGTT
TACAGAAACAGAGGAAGATGTCAGCAGCCTGAGAGAAGCTGAAGCCTTGAAAAAAGAAATGCCAGTGAAAGAGGACAGGC
ACAGGAGTATACTGAAGATGAAGTTCCGGCAAATGTGGGAGGCCTGGCACGGAAACAGCAAAGAGGTCCAAGCTGTGGCT
CAGAGATACACGACGCTGATCCCATTCAGCAACCCCAGGATGCTTCCCGGGCCCTTCCCAACACGGTGGTGCTGCACGGC
CCTGCCGGCCTTGCGAAAACCACGCTCACCAAGAAATTAATGTTGGACTGGACAGAGGACAACCTCGGCCACAAATTCAA
ATACGCTTTCTACCTCAGCTGCAAAATGATCAGCCGCCTGGGCCTGTGCAGTTTTGCAGAGCTGGTCTTCAGGGACTGGC
CGGAATTTCAGGATGACATTCCAAACATCCTAGCCGAAGCACAGAAAATCCTGTTCGTGGTCAACGCCCTTGATGAGCTG
GGAGCCCCACCCAGGGCGCTGATCCACAATATCTGCGCGGACTGGCTGAAGCCGAAGCCGGTGCCGGTCCTCCTGGGGAG
TTTGCTGAAAAGGAAGATGTTACCCAAGGCCGCCCTGTTGGTCACCACGCGGTCCTGAGCCCTGAGGGACCTCCAGCCCC
TGATGAAGCAGCCCATCTACATAAGGGTGGAGGGGTTCCTGGAGGAGGACAGGAGGGCCTATTTCCTGAGATACTTTGGA
GAGGAGGACCAAGCCATGCGTGCCTTTGAGCTGATAAGAAGCAACACAGCCCTGTTCCAGCTGGGCTCGGCGCCTGCGGT
GTGCTAAATGGTGTACACGAGTCTGAAGCTGCAGATGGAGAACGGGGAGGACCCGGCCCCCAACTGCCACACCCGCACGG
GGCTGTTCCTGCACTTTCTCTGCGGCCACTTCCCGAAGGATTCACAGCTCGGGTGCACGCTGCGGGCGCTGAGCCTCCTG
GCTACACAGGGCCTGTGGGCGCAGATGTCCACGTTCCACAGAGAGGACCTGGAAAGCTTCGGGTTGCAGGAGTCCCATCT
CCGCCCATTCCTGGACAGAGGCATCCTCCGCCAGGATAGAGACTCTAAAGACTGCTACTCCTTCCTCCACCTCAGCTTCC
AGCAGCTTTTCACTGCATTGTTCTACGCCCTGGAGGAGGAGGAGGAGGACAGGGATGGCCACGCCTGGGACATTAAGGAC
GTGCAAAAGCTGCTTTCTGGAGAAGAACGACTCCAGAACCCCGACCTGATCCAAGCAGGACACTTCTTATTCGGCCTTGC
CAACGAGAAGAGAGCCACAGAGTTGGAGACCACTTTTGGCTGCGTGATGTCACAGGAGATCAAACAGGAATTACTGCAGT
GCGACATCATTTGTGAGGAGAACAGATACTCAACCATGATGGACCTGAAGGAGGTCTTACACTGTCTGTACGAGTCTCAG
GAAGAGGAGCTGGTGAAGCGGGTGATGGCCCCGTTGAAAGAAATATCCCTGCATTTAAGTGCCGCAGACATTGTGCCCTC
TTCGTTCTGCCTCAAGCATTGTCGAAACTTGGAGAAAATGTCACTGCAGGTGATAAAGACAAAGCTCCCAGAGAATGTCA
CTGCCTCTGAATCAGATGCTGAGGTTGAGAGATCCCAGGATGATCAACACATGCTTCCTTTCTGGACGGATCTTTGTTCC
ATATTTGGCTCAAACAAGGATCTAATCATTATAGAAATTAATAATAGCTTCCTTAGTGCCTCACTGTTAAGGATTCTACG
TGAACAAATAGCTTCTGACAACTGTCATCTCCAGAGAGTGGTGATCAAAAACATTTCCCCAGCTGATGCTTATCGGAACC
TCTGCCTAGCTCTTCAAGGTCACAAGAGTGTAACACATCTAAGACTTCGAGGCAGTGCCCAGAATGATACACTTCCTGCA
CTGTGTGAAGTCCTGAAGCACCCAAAATGTAACCTGCAGTATCTCGGGTTGGTGTCTTGTTCT

Alignment

ORF - retro_cjac_3184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.1 %
• Parental protein coverage: 86.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ETIRKGEPEPVDLDEMLVHFKAEAQAFTETEEDVSSLREAEALKKEMPGKEDRHRSILKMKFRQMWEAWP
          ETIRKGEP.PVDLDEMLV....EAQAFTETEEDVSSLREAEALKKEMP.KEDRHRSILKMKFRQMWEAW.
Retrocopy ETIRKGEPKPVDLDEMLVRLETEAQAFTETEEDVSSLREAEALKKEMPVKEDRHRSILKMKFRQMWEAWH

Parental  GASRGVQAVAQRYMTLIPFSNPRILPGPFP-HTVVLHGPAGLGKTTLAKRLMLDWTEDNLSHKFKYAFYL
          G.S..VQAVAQRY.TLIPFSNPR.LPGPFP..TVVLHGPAGL.KTTL.K.LMLDWTEDNL.HKFKYAFYL
Retrocopy GNSKEVQAVAQRYTTLIPFSNPRMLPGPFP<NTVVLHGPAGLAKTTLTKKLMLDWTEDNLGHKFKYAFYL

Parental  SCKRLSRLGLCSFAELVFRDWPELQGDVPDILAQAQKILFVVDGLDELGAPPGALIHDICGDWLKPKPVP
          SCK..SRLGLCSFAELVFRDWPE.Q.D.P.ILA.AQKILFVV..LDELGAPP.ALIH.IC.DWLKPKPVP
Retrocopy SCKMISRLGLCSFAELVFRDWPEFQDDIPNILAEAQKILFVVNALDELGAPPRALIHNICADWLKPKPVP

Parental  VLLGSLLKRKMLPKAALLVTTRSWALRDLRPLMEQPIYIRVEGFLEEDRRAYFLTHFGEEDQATRAFELM
          VLLGSLLKRKMLPKAALLVTTRS.ALRDL.PLM.QPIYIRVEGFLEEDRRAYFL..FGEEDQA.RAFEL.
Retrocopy VLLGSLLKRKMLPKAALLVTTRS*ALRDLQPLMKQPIYIRVEGFLEEDRRAYFLRYFGEEDQAMRAFELI

Parental  RSNAALFQLGSAPAVCWMVCTSLKLQMENGEDPATTCHTRTGLFLHFLCSRFPKGAQLGGTLRALSILAA
          RSN.ALFQLGSAPAVC.MV.TSLKLQMENGEDPA..CHTRTGLFLHFLC..FPK..QLG.TLRALS.LA.
Retrocopy RSNTALFQLGSAPAVC*MVYTSLKLQMENGEDPAPNCHTRTGLFLHFLCGHFPKDSQLGCTLRALSLLAT

Parental  QGLWAQMSVFHREDLESFRVQESDLRPFLDRGILRQDRDSKDCYSFLHLSFQQFFTALFYALEKEEEDRD
          QGLWAQMS.FHREDLESF..QES.LRPFLDRGILRQDRDSKDCYSFLHLSFQQ.FTALFYALE.EEEDRD
Retrocopy QGLWAQMSTFHREDLESFGLQESHLRPFLDRGILRQDRDSKDCYSFLHLSFQQLFTALFYALEEEEEDRD

Parental  GHAWDIGDVQRLLSGEERVQNPDLIQAGHFLFGLANEKRAAELETTFGCVMSREIKQELLRCDIICEEDR
          GHAWDI.DVQ.LLSGEER.QNPDLIQAGHFLFGLANEKRA.ELETTFGCVMS.EIKQELL.CDIICEE.R
Retrocopy GHAWDIKDVQKLLSGEERLQNPDLIQAGHFLFGLANEKRATELETTFGCVMSQEIKQELLQCDIICEENR

Parental  YSTLTDLKEVLHCLYESQEGELVKAVMAPLKEISVHLSAADIVPSSFCLKHCRNLEKMSLQVIKAKLPEN
          YST..DLKEVLHCLYESQE.ELVK.VMAPLKEIS.HLSAADIVPSSFCLKHCRNLEKMSLQVIK.KLPEN
Retrocopy YSTMMDLKEVLHCLYESQEEELVKRVMAPLKEISLHLSAADIVPSSFCLKHCRNLEKMSLQVIKTKLPEN

Parental  VTASESDAEAERSQDDQHLLPFWTDLCSVFGSNKDLITLEINNSFLSASLLRILCEQIASDTCHLQRVVI
          VTASESDAE.ERSQDDQH.LPFWTDLCS.FGSNKDLI..EINNSFLSASLLRIL.EQIASD.CHLQRVVI
Retrocopy VTASESDAEVERSQDDQHMLPFWTDLCSIFGSNKDLIIIEINNSFLSASLLRILREQIASDNCHLQRVVI

Parental  KNISPADAYRNLCLALQGQKTVTYLRLRGSAQNDTLPALCEVLRHPKCNLQYLGYTSSS
          KNISPADAYRNLCLALQG.K.VT.LRLRGSAQNDTLPALCEVL.HPKCNLQYLG..S.S
Retrocopy KNISPADAYRNLCLALQGHKSVTHLRLRGSAQNDTLPALCEVLKHPKCNLQYLGLVSCS

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	0.58 RPM	0.02 RPM
SRP051959_heart	0.77 RPM	0.00 RPM
SRP051959_kidney	0.60 RPM	0.00 RPM
SRP051959_liver	0.30 RPM	0.00 RPM
SRP051959_lung	1.09 RPM	0.00 RPM
SRP051959_lymph_node	2.31 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.28 RPM	0.00 RPM
SRP051959_spleen	1.49 RPM	0.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3184 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3184 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,