RetrogeneDB ID: retro_cjac_3012

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:106778564..106779777(-)
• Located in intron of: ENSCJAG00000022946

Retrocopy information

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

Parental gene information

• Parental gene symbol: RANBP3
• Ensembl ID: ENSCJAG00000016791
• Aliases: None
• Description: None

Sequence

>retro_cjac_3012
GAGCCCAGGGAAAAGCAGCGGAGCGTGCTTCCTATGGCAGTGATCAGGCCCCGCAGCCAAAGGCGCTGTCCCAGATGGTC
CCCAGCAGTGGCACCAATGGGGTCAGCCTCCCAGCCGACCGCACGGAGGCCGTGCCAGCAGCATCCCCTGACAACCCTGC
AGGGAAGAGTCCTTCCCAAGCTGCCGACGAGGTGTGTGCACTTGAGGAGAAGGAGCCCCAGAAAAATGAGTCCAGCGATG
CCTCTGAAGAGGAAGCCTGTGAGAAAAAAGACCCCACCACACAACAAGCGTTTGTACTTGGGCAGAACTTGAGGGACGGA
GTTAAGCTGATCAATGAGAGTGTGGACAAAGCCGACATGGAGAGTGCTGGACACCCCAGCGCAGACACACCGGCCGGACA
AACTATTTCCTTCAGCGTATCAGTTCCAGTTTAGAGAACTCAACCAATAGTGCCGATGCCTCCAGCAACAAACTCGTATT
TGGCCAGAATTTGAGTGAGCGAGTTTTGAGCTTTCCAAAATTAAATGAGGTCAGTTCAGATGCCAGTAGGGAAAATGCAG
CTGCCAACGCGGGGTCCACGTCCTCATCCCAAGAGGCCACCCCCGAGAAGGAGTCCCTGGCCAAGTCGGCAGCCGCCTAC
ACCAAGGCAAAGGAGCGGAAGTGCTTGTTGGAAAAAAGTGGAAGTCATCACGGGGAGGAGGCGGAGAGCAACGTGTTACA
GATGTAGTGCAAGCTCTTTGTCTTTGACAAGGCCTCACAGTCCTGGGTGGAGAGAGGCCGGGGGCTGCTCAGACTCAATG
ACATGGCGTCCACTGACGATGGCACGCTACAGTCCCGACTAGTAATGCGGACCCAGGGGAGCCTGCGACTGATCCTCAAC
ACCAAGCTGTGGGCCCAGATGCAGATCGACAAGGCCAGCGAGAAGAGCATCCGCATCATGGCCATGGACACCGAGGACCA
GGGCGGGAAGGTCTTCCTGATCTCGGCCAGCTCCAAGGACACAGGTCAGCTGTATGCAGCCCTGCAGCACCACATCCTGG
CCTTAGGCAGCCGCGGGGAGTGGGAGCAGGTGGCCAAGATGCCCGCCCCGGAGCCTGGAGCAGCCCCATCCAACGAGGAG
GATGACAGTGACGACGACGATGTCCTGGCTCCTTCAGGGGCAACTGCAGCCGGTGCTAATGACGAAGGGGACGGGCAGAC
GACTGGGAGCACA

Alignment

ORF - retro_cjac_3012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.57 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KPKEQQRSVLRPAVL-QAPQPKALSQTVPSSGTNGVSIPADCTEAVPAASPDNPARRSPSEAADEVCALE
          .P.E.QRSVL..AV..QAPQPKALSQ.VPSSGTNGVS.PAD.TEAVPAASPDNPA..SPS.AADEVCALE
Retrocopy EPREKQRSVLPMAVI<QAPQPKALSQMVPSSGTNGVSLPADRTEAVPAASPDNPAGKSPSQAADEVCALE

Parental  EKEPQKNESGNASEEEACEKKDPATQQAFVFGQNLRDRVKLINESADEADMENAGHPSADTPAA-TNYFL
          EKEPQKNES..ASEEEACEKKDP.TQQAFV.GQNLRD.V.................PSADTPA..TNYFL
Retrocopy EKEPQKNESSDASEEEACEKKDPTTQQAFVLGQNLRDGVXXXXXXXXXXXXXXXXXPSADTPAG<TNYFL

Parental  QYISSSLENSTNSADASSNKFVFGQNMSERVLSFPKLNEVSSDASRENAAAESGSESSSQEATPEKESLA
          Q.ISSSLENSTNSADASSNK.VFGQN.SERVLSFPKLNEVSSDASRENAAA..GS.SSSQEATPEKESLA
Retrocopy QRISSSLENSTNSADASSNKLVFGQNLSERVLSFPKLNEVSSDASRENAAANAGSTSSSQEATPEKESLA

Parental  ESAAAYTKATARKCLLEK-VEVITG-EEAESNVLQMQCKLFVFDKASQSWVERGRGLLRLNDMASTDDGT
          .SAAAYTKA..RKCLLEK.VEVITG.EEAESNVLQM.CKLFVFDKASQSWVERGRGLLRLNDMASTDDGT
Retrocopy KSAAAYTKAKERKCLLEK>VEVITG<EEAESNVLQM*CKLFVFDKASQSWVERGRGLLRLNDMASTDDGT

Parental  LQSRLVMRTQGSLRLILNTKLWAQMQIDKASEKSIRITAMDTEDQGVKVFLISASSKDTGQLYAALHHRI
          LQSRLVMRTQGSLRLILNTKLWAQMQIDKASEKSIRI.AMDTEDQG.KVFLISASSKDTGQLYAAL.H.I
Retrocopy LQSRLVMRTQGSLRLILNTKLWAQMQIDKASEKSIRIMAMDTEDQGGKVFLISASSKDTGQLYAALQHHI

Parental  LALRSRVEQEQEAKMPAPEPGAAPSNEEDDSDDDDVLAPSGATSAGAGDEGDGQTTGST
          LAL.SR.E.EQ.AKMPAPEPGAAPSNEEDDSDDDDVLAPSGAT.AGA.DEGDGQTTGST
Retrocopy LALGSRGEWEQVAKMPAPEPGAAPSNEEDDSDDDDVLAPSGATAAGANDEGDGQTTGST

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	7.52 RPM
SRP051959_heart	0.02 RPM	10.72 RPM
SRP051959_kidney	0.00 RPM	10.87 RPM
SRP051959_liver	0.02 RPM	5.24 RPM
SRP051959_lung	0.00 RPM	13.88 RPM
SRP051959_lymph_node	0.02 RPM	13.24 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.06 RPM
SRP051959_spleen	0.00 RPM	11.34 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3012 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3012 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3012 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	ENSCJAG00000016791	1 retrocopy	retro_cjac_3012 ,