RetrogeneDB ID: retro_cjac_769

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:27929010..27930411(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUPL1
• Ensembl ID: ENSCJAG00000019231
• Aliases: None
• Description: nucleoporin like 1 [Source:HGNC Symbol;Acc:20261]

Sequence

>retro_cjac_769
ATGTCCATGGGGTTCTCCTTCGGGTCCAGGACTTTGGACCCCACCACCGTAGCCCCTGGCAGGACCAGCACAGGTGGCAG
TTTCTCCTTTGGGACGGGAGTGTCTAGCAACCCTTCTGTGGGGCTCAATTTTGGAACTCTTGGAGGTCCTGCAACTCCAG
CAACTACACCTGCTCCTTCAAGCTGGTTTTGGAACCAGGCTCTTTGGATCTAAACCTGCTACTGGGTTCACTCTAGGAGG
AACAAATACAGGGACACCAGCCACTACATCTGCCCCTACAACAGGCTTCAGTTTAGGATTCAATAAACCTGCAGCATCTG
CCACACCATTTGCTCTACCTATTACTTCTACCTCAGCTAGCAGTCTCACTCTTTCCTCTGCTCTGACATCAACTCCAGCA
GCTTCCACAGGATTTACCCCAAATAATTTGGGTGGGACAATAGCCACAACTACAACTGCATCAACAGGCCTCTCTCTAGG
GGGAGCCTTAGCTGGTTTGGGAGGTTCACTTTTCCAGAGCACAGACACAGCAACATCAGGACTAGGACAGAATGCTTTAG
GCTTGACTTTGGGAACTACAGCAGCTACTTCAAGTGCAGGCAATGAAGGCCTTGGTGGCATAGATTTTAGTAGCTCCTCA
GATAAAAAGAGTGATAAAACAGGAACAAGACCAGAGGATAGTAAAGCTCTGAAGGATGAAAATCTACCTCCTGTCATCTG
CCAGGATGTTGAAAATCTCCAGAAATTTGTCAAGGAGCAGAAACAAGCTCAAGAAGAAATTAATAGAATGTCTTCAAAAG
CAATGCTTAAGGTACAAGAAGATATTAAAGCTCTGAAGCAGCTCCTGTCATTGGCTGCCAATAGACCACAGAGAAACACT
CTCAACATTGACAAATTGAAAATAGAAACTGCTCAGGAGTTAAAGAATGCTGAAATAGCTTTAAAAACCTAGAAGGCACC
ACCTGGACTTCAACATAAATATGCAGCTCCTGCTGACTACTTCAGAATCTTGGTTCAGCAATTTGAGGTACAGCTTCAGC
AATACAGACAACAGATTGAAGAACTAGAAAATTATCTTGCCACTCAAGCAAATAATTCACATATAACCCCTCAAGATTTG
TCAATGGCTATGCAGTAAATTTAAAAAACATTTGTAGCTTTAGCAGCACAACTTCAGTCTATTCATGAAAATGTAAAGGT
TCTGAAAAACAGTACCTTGGCTACAGGAAAATGTTCTTGGGAGATGCTGTTGATGTGTTTGAAGCAAGACGAGCAGAAGC
CAAGAAGTGGCAGAACACACCCAGAGTTACTACCGGACCCACCCCTTTCAGCACCATGCCAAATGCAGCAGCCATTGCCG
TGGCTGCAACACTTACACAGCAGCAACAGCCTGCTACAGGT

Alignment

ORF - retro_cjac_769 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.54 %
• Parental protein coverage: 79.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSTGFSFGSGTLGSTTVAPGGTGTGGGFSFGTGASSNPSVGLNFGTLGSTATPTTTSAPSS-GFGTGLFG
          MS.GFSFGS.TL..TTVAPG.T.TGG.FSFGTG.SSNPSVGLNFGTLG..ATP.TT.APSS.GFGT.LFG
Retrocopy MSMGFSFGSRTLDPTTVAPGRTSTGGSFSFGTGVSSNPSVGLNFGTLGGPATPATTPAPSS>GFGTRLFG

Parental  SKPATGFTLGGTNTGTPATTSAPTTGFSLGFNKPAASATPFALPITSTSASGLTLSSALTSTPAASTGFT
          SKPATGFTLGGTNTGTPATTSAPTTGFSLGFNKPAASATPFALPITSTSAS.LTLSSALTSTPAASTGFT
Retrocopy SKPATGFTLGGTNTGTPATTSAPTTGFSLGFNKPAASATPFALPITSTSASSLTLSSALTSTPAASTGFT

Parental  LNNLGGTTATTTTASTGLSLGGALAGLGGSLFQSTNTATSGLGQNALGLTLGTTAATSAAGNEGLGGIDF
          .NNLGGT.ATTTTASTGLSLGGALAGLGGSLFQST.TATSGLGQNALGLTLGTTAATS.AGNEGLGGIDF
Retrocopy PNNLGGTIATTTTASTGLSLGGALAGLGGSLFQSTDTATSGLGQNALGLTLGTTAATSSAGNEGLGGIDF

Parental  SSSSDKKSDKTGTRPEDSKALKDENLPPVICQDVENLQKFVKEQKQVQEEISRMSSKAMLKVQEDIKALK
          SSSSDKKSDKTGTRPEDSKALKDENLPPVICQDVENLQKFVKEQKQ.QEEI.RMSSKAMLKVQEDIKALK
Retrocopy SSSSDKKSDKTGTRPEDSKALKDENLPPVICQDVENLQKFVKEQKQAQEEINRMSSKAMLKVQEDIKALK

Parental  QLLSLAANGLQRNTLNIDKLKIETAQELKNAEIALRTQKTPPGLQHEYAAPADYFRILVQQFEVQLQQYR
          QLLSLAAN..QRNTLNIDKLKIETAQELKNAEIAL.T.K.PPGLQH.YAAPADYFRILVQQFEVQLQQYR
Retrocopy QLLSLAANRPQRNTLNIDKLKIETAQELKNAEIALKT*KAPPGLQHKYAAPADYFRILVQQFEVQLQQYR

Parental  QQIEELENHLATQANNSHITPQDLSMAMQKIYQTFVALAAQLQSIHENVKVLK-EQYLGYRKMFLGDAVD
          QQIEELEN.LATQANNSHITPQDLSMAMQ.I..TFVALAAQLQSIHENVKVLK..QYLGYRKMFLGDAVD
Retrocopy QQIEELENYLATQANNSHITPQDLSMAMQ*I*KTFVALAAQLQSIHENVKVLK<KQYLGYRKMFLGDAVD

Parental  VFEARRAEAKKWQNTPRVTTGPTPFSTMPNAAAVAMAATLTQQQQPATG
          VFEARRAEAKKWQNTPRVTTGPTPFSTMPNAAA.A.AATLTQQQQPATG
Retrocopy VFEARRAEAKKWQNTPRVTTGPTPFSTMPNAAAIAVAATLTQQQQPATG

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	0.07 RPM	22.36 RPM
SRP051959_heart	0.12 RPM	21.29 RPM
SRP051959_kidney	0.22 RPM	24.27 RPM
SRP051959_liver	0.28 RPM	14.66 RPM
SRP051959_lung	0.20 RPM	23.99 RPM
SRP051959_lymph_node	0.07 RPM	23.20 RPM
SRP051959_skeletal_muscle	0.24 RPM	24.90 RPM
SRP051959_spleen	0.23 RPM	22.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_769 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_769 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_769 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019231	1 retrocopy	retro_cjac_769 ,