RetrogeneDB ID: retro_cjac_308

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:103313552..103315475(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000011116
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LRRC4B
• Ensembl ID: ENSCJAG00000017224
• Aliases: None
• Description: None

Sequence

>retro_cjac_308
ATGTTGAACAAGATGACCTTACATCCACAGCAGATAATGATAGGTCCTAGGTTTAACAGGGCCCTATTTGACCCCCTGCT
TGTGGCGCTGCTGGCTCTTCAACTTCTTGTGGTGGCTGGTCTGGTGCGGGCTCAGACCTGCCCTTCTGTGTGCTCCTGCA
GCAACCAATTCAGCAAGGTGATTTGCGTTCGGAAAAACCTGCGTGAGGTTCCGGATGGCATCTCCACCAACACACGGCTG
CTGAACCTCCATGAGAACCAAATCCAGATCATCAAAGTGAACAGCTTCAAGCACTTGAGGCACTTGGAAATCCTACAGTT
GAGTAGGAACCATATCAGAACCATTGAAATTGGGGCTTTCAATGGTCTGGCGAACCTCAATACTCTGGAACTTTTTGACA
ATCGTCTTACTACCATCCCGAATGGAGCTTTTGTATACTTATCTAAACTGAAGGAGCTCTGGTTGCGAAACAACCCCATT
GAAAGCATCCCTTCTTATGCTTTTAACAGAATTCCTTCTTTGCGCCGACTAGACTTAGGGGAATTGAAAAGACTTTCATA
CATCTCAGAAGGTGCCTTTGAAGGTCTGTCCAACTTGAGGTATTTGAACCTTGCCATGTGCAACCTTCGGGAAATACCTA
ACCTCACGCCGCTCATAAAACTAGATGAGCTGGATCTTTCTGGGAATCATTTATCTGCCATCAGGCCTGGCTCTTTCCAG
GGTTTGATGCACCTTCAAAAACTGTGGATGATACAGTCCCAGATTCAAGTGATTGAACGGAATGCCTTTGACAACCTTCA
GTCACTAGTGGAGATCAACCTGGCACACAATAATCTAACATTATTGCCTCATGACCTCTTCACTCCCTTGCATCATCTAG
AGCGGATACATCTACATCACAACCCTTGGAACTGTAACTGTGACATACTGTGGCTCAGCTGGTGGATAAAAGACATGGCC
CCCTCCAACACAGCTTGTTGTGCCCGGTGTAACACTCCTCCCAATCTAAAGGGGAGGTACATTGGAGAGCTCGACCAGAA
TTATTTCACATGCTATGCTCCAGTGATTGTGGAGCCCCCTGCAGACCTCAATGTCACTGAAGGCATGGCAGCTGAGTTGA
AATGTCGGGCCTCCACCTCCCTGACATCTGTATCTTGGATTACTCCAAATGGAACAGTCATGACACATGGGGCATACAAA
GTGAGGATAGCTGTGCTCAGTGATGGTACGTTAAATTTCACAAATGTAACTGTGCAAGATACAGGCATGTACACATGTAT
GGTGAGTAATTCCGTTGGGAATACTACCGCTTCAGCCACCCTGAATGTTACTGCGGCAACCACTACTCCTTTCTCTTACT
TTTCAACTGTCACAGTAGAGACTATGGAACCGTCTCAGGATGAGGCACGGACCACAGATAACAATGTGGGTCCCACTCCA
GTGGTTGACTGGGAGACCACCAATGTGACCACCTCTCTCATGCCACAGAGCACAAGGTCAACAGAGAAAACCTTCACCAT
CCCAGTGACTGATATAAACAGTGGGATCCCAGGAATCGATGAGGTCATGAAGACTACCAAAATTATCATTGGGTGTTTTG
TGGCCATCACACTCATGGCTGCAGTGATGCTGGTCATTTTCTACAAGATGAGGAAGCAGCACCATCGGCAAAACCATCAT
GCCCCAACAAGGACTGTTGAAATCATTAATGTGGATGATGAGATTACGGGAGACACACCCATGGAAAGCCACCTGCCCAT
GCCTGCTATCGAGCATGAGCACCTAAATCACTATAACTCATACAAATCTCCCTTCAACCACACAACAACAGTTAACACAA
TAAATTCAATACACAGTTCAGTGCATGAACCGTTATTGATCCGAATGAACTCTAAAGACAATGTACAAGAGACTCAAATC
TAA

Alignment

ORF - retro_cjac_308 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.8 %
• Parental protein coverage: 80.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAVTSAAAGGSPPATSCPEACSCSNQASRVICTRRELAEVPASIPVNTRYLNLQENGIQVIRTDTFKHLR
          .A.......G...A..CP..CSCSNQ.S.VIC.R..L.EVP..I..NTR.LNL.EN.IQ.I....FKHLR
Retrocopy LALQLLVVAGLVRAQTCPSVCSCSNQFSKVICVRKNLREVPDGISTNTRLLNLHENQIQIIKVNSFKHLR

Parental  HLEILQLSKNLVRKIEVGAFNGLPSLNTLELFDNRLTTVPTQAFEYLSKLRELWLRNNPIESIPSYAFNR
          HLEILQLS.N..R.IE.GAFNGL..LNTLELFDNRLTT.P..AF.YLSKL.ELWLRNNPIESIPSYAFNR
Retrocopy HLEILQLSRNHIRTIEIGAFNGLANLNTLELFDNRLTTIPNGAFVYLSKLKELWLRNNPIESIPSYAFNR

Parental  VPSLRRLDLGELKRLEYISEAAFEGLVNLRYLNLGMCNLKDIPNLTALVRLEELELSGNRLDLIRPGSFQ
          .PSLRRLDLGELKRL.YISE.AFEGL.NLRYLNL.MCNL..IPNLT.L..L.EL.LSGN.L..IRPGSFQ
Retrocopy IPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAMCNLREIPNLTPLIKLDELDLSGNHLSAIRPGSFQ

Parental  GLTSLRKLWLMHAQVATIERNAFDDLKSLEELNLSHNNLMSLPHDLFTPLHRLERVHLNHNPWHCNCDVL
          GL..L.KLW....Q...IERNAFD.L.SL.E.NL.HNNL..LPHDLFTPLH.LER.HL.HNPW.CNCD.L
Retrocopy GLMHLQKLWMIQSQIQVIERNAFDNLQSLVEINLAHNNLTLLPHDLFTPLHHLERIHLHHNPWNCNCDIL

Parental  WLSWWLKETVPSNTTCCARCHAPAGLKGRYIGELDQSHFTCYAPVIVEPPTDLNVTEGMAAELKCRTGTS
          WLSWW.K...PSNT.CCARC..P..LKGRYIGELDQ..FTCYAPVIVEPP.DLNVTEGMAAELKCR..TS
Retrocopy WLSWWIKDMAPSNTACCARCNTPPNLKGRYIGELDQNYFTCYAPVIVEPPADLNVTEGMAAELKCRASTS

Parental  MTSVNWLTPNGTLMTHGSYRVRISVLHDGTLNFTNVTVQDTGQYTCMVTNSAGNTTASATLNVSA--VDP
          .TSV.W.TPNGT.MTHG.Y.VRI.VL.DGTLNFTNVTVQDTG.YTCMV.NS.GNTTASATLNV.A....P
Retrocopy LTSVSWITPNGTVMTHGAYKVRIAVLSDGTLNFTNVTVQDTGMYTCMVSNSVGNTTASATLNVTAATTTP

Parental  NTYFTTVTVETLETQPGEEALQPRGTEKEPPGPTTDGVSSSTTAPAPRSSRPTEKAFTVPITDVTENALK
          ..YF.TVTVET.E..P.............P...........TT...P.S.R.TEK.FT.P.TD.......
Retrocopy FSYFSTVTVETME--PSQDEARTTDNNVGPTPVVDWETTNVTTSLMPQSTRSTEKTFTIPVTDI-NSGIP

Parental  DLDDVMKTTKIIIGCFVAITFMAAVMLVAFYKLRKQHQLHKHHGPTRTVEIINVEDEL
          ..D.VMKTTKIIIGCFVAIT.MAAVMLV.FYK.RKQH....HH.PTRTVEIINV.DE.
Retrocopy GIDEVMKTTKIIIGCFVAITLMAAVMLVIFYKMRKQHHRQNHHAPTRTVEIINVDDEI

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	0.20 RPM	0.07 RPM
SRP051959_heart	0.58 RPM	0.11 RPM
SRP051959_kidney	0.82 RPM	0.04 RPM
SRP051959_liver	0.00 RPM	0.02 RPM
SRP051959_lung	0.08 RPM	0.02 RPM
SRP051959_lymph_node	0.09 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.13 RPM	0.00 RPM
SRP051959_spleen	0.15 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_308 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_308 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_308 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017224	1 retrocopy	retro_cjac_308 ,
Otolemur garnettii	ENSOGAG00000002426	1 retrocopy	retro_ogar_171,