RetrogeneDB ID: retro_cjac_397

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:56885310..56886701(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEN1
• Ensembl ID: ENSCJAG00000002716
• Aliases: None
• Description: None

Sequence

>retro_cjac_397
GGCACCAAATTTGACAGCTCTGATGTGGCCTTTGCTGTGGTTGGGGTTTGCCAGGCCTTGGGTGTCTGGGATGTCCTCCT
CGCCCTGTCTGAGGATCATGCCTGGGTAGTGTTTGGACCCAATGGGGAGCAGACAGCTGAGGTCACCTAGCATGGCAAGG
GCATTAAGAACTGCAGGTGCCAGACGGTCAACACTGGTGTGGCTAAGCGGAGCTGGCTGTACCTGAAAGGATCATACATG
CGCTGTGACCGCAAGGTGGAGATGGCGTTCATGGTGTGTGCCATCAGCTCTTCCATTGACCTATATACTGACTCATTAGA
GCTGCTGCAGGTACAGCAGAAGCTGCTCTGGCTGCTCTATGACCTGGGACATCTGGAAAGGTACCCCATGGCCTTAGGGA
ACTTGGAAGATCTAGAGGATCTGGAGCCTACTCCTGGCCAGCCAGACCCACTCACCTTCTACCACAAGGGCATTGCCTCA
GCTAAAACCTATCAGGATGAACACATCTACCCCTGCATGTACGTGGCTGGCTAACACTGTCACAACCAAAATGTGTGTGA
AGCCCTGCAGGCCTGGGCTGACACGGCCACTGTCATGCAGGACTACAACTACTGCCGGGAAGACGAGGAGATCCACAAGG
AGTTCTTTGAAGTAGCCAATGATGTCATCCCCAGCCTGCTGAAGGAGGCAGCCAGCTTGCTAGAGGTGGACATGGAGCCG
TCGCGGGGAGCAGAGCCAGGGCACCCAGAGCCAAGATTCTGTCTCCAGGACCCTGAGTGCTTTGCCCACCTGCTGCGATT
CTGTGGCAGGATCTGCAAATGGGAGGAGGGCAGTCCCACGCCTGTGTTGCATGTGGGCTGGGCCACCTTCCTTGTGCAGT
CCCTAGGCTGTTTCGAGGAACAGGTGCAGCAGAAGGTGAGCATAATGAGCCGGGAGGCCGAGGAGGCTGAGGCAGAGCAG
CTGTGGGTTGAGGAAGCCCAGGAAGGCCGGTGGCAGGCCCCACGGCGGTCGTCCAAGCTAGAGGAGCCCCCGCCCCCCAA
GAAGCCATCACTGGACAAGGGCCCAGGCGCCAGCCAGGGTGCGGTGTCAGGACTTCCCCCACCCCACCCCCAGAAACCCC
TGGGACAGTCCCTGGCACAGATCAAGGCCCTGAAGGTGGCAGCACGGCTCAGGCGCCAGCGCCTGCAGCATCACCACTGC
TGGAAGGTCCAGTGCTCACTTTCCAGAACAAGAAGATGAAGGGCATGAAGGAGCTGCTGGTGGCCACCAAGGTCAACTCA
AGCGCCATCAAGCTGCAACTCACGGCGCAGTCCCAAGTTCAGATGAAGAAGCAGAAGGTGTCCACCCCTAGTGAATACAC
TCTGACTTTCCGCAAGTGGCAGCGCAAAGGC

Alignment

ORF - retro_cjac_397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.06 %
• Parental protein coverage: 99.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GTKLDSSGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAEVTWHGKGNEDRRGQTVNAGVAER
          GTK.DSS.VAFAVVG.CQALG..DV.LALSEDHAWVVFGPNGEQTAEVT.HGKG....R.QTVN.GVA.R
Retrocopy GTKFDSSDVAFAVVGVCQALGVWDVLLALSEDHAWVVFGPNGEQTAEVT*HGKGIKNCRCQTVNTGVAKR

Parental  SWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHTDSLELLQLQQKLLWLLYDLGHLERYPMALGNLADLEE
          SWLYLKGSYMRCDRK.E.AFMVCAI..SIDL.TDSLELLQ.QQKLLWLLYDLGHLERYPMALGNL.DLE.
Retrocopy SWLYLKGSYMRCDRKVEMAFMVCAISSSIDLYTDSLELLQVQQKLLWLLYDLGHLERYPMALGNLEDLED

Parental  LERTPGRPDPLTLYHKGFPLIWTVYRVKCVEHCGGLAGYHCRNRNVREALQDWADTATVIQDYNYCREDE
          LE.TPG.PDPLT.YHKG.....T.Y.......C...AG.HC.N.NV.EALQ.WADTATV.QDYNYCREDE
Retrocopy LEPTPGQPDPLTFYHKGIASAKT-YQDEHIYPCMYVAG*HCHNQNVCEALQAWADTATVMQDYNYCREDE

Parental  EIYKEFFEVANDVIPNLLKEAASLLEAGEE-RPGEQSQGTQSQGSA-LQDPECFAHLLRFYDGICKWEEG
          EI.KEFFEVANDVIP.LLKEAASLLE...E.R.GEQSQGTQSQ.S..LQDPECFAHLLRF...ICKWEEG
Retrocopy EIHKEFFEVANDVIPSLLKEAASLLEVDME>RRGEQSQGTQSQDSV<LQDPECFAHLLRFCGRICKWEEG

Parental  SPTPVLHVGWATFLVQSLGRFEGQVRQKVRIVSREAEAAEAEEPWGEEAREGRRRGPRRESKPEEPPPPK
          SPTPVLHVGWATFLVQSLG.FE.QV.QKV.I.SREAE.AEAE..W.EEA.EGR...PRR.SK.EEPPPPK
Retrocopy SPTPVLHVGWATFLVQSLGCFEEQVQQKVSIMSREAEEAEAEQLWVEEAQEGRWQAPRRSSKLEEPPPPK

Parental  KPALDKG----QGAVSGPP----RKPPG-TVPGTARGPEGGSTAQAPAPAASPPLEGPVLTFQSEKMKGM
          KP.LDKG....QGAVSG.P.....KP.G.TVPGT..GPEGGSTAQAPAPAASP.LEGPVLTFQ..KMKGM
Retrocopy KPSLDKGPGASQGAVSGLPPPHPQKPLG<TVPGTDQGPEGGSTAQAPAPAASPLLEGPVLTFQNKKMKGM

Parental  KELLVATKINSSAIKLQLTAQSQVQMKKQKVSTPSDYTLSFLKRQRKG
          KELLVATK.NSSAIKLQLTAQSQVQMKKQKVSTPS.YTL.F.K.QRKG
Retrocopy KELLVATKVNSSAIKLQLTAQSQVQMKKQKVSTPSEYTLTFRKWQRKG

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	1.86 RPM
SRP051959_heart	0.00 RPM	2.25 RPM
SRP051959_kidney	0.02 RPM	2.60 RPM
SRP051959_liver	0.00 RPM	2.27 RPM
SRP051959_lung	0.00 RPM	2.93 RPM
SRP051959_lymph_node	0.00 RPM	3.47 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.83 RPM
SRP051959_spleen	0.00 RPM	2.46 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_397 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_397 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_397 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002716	1 retrocopy	retro_cjac_397 ,