RetrogeneDB ID: retro_cjac_3896

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286126.1:7487..8584(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD23A
• Ensembl ID: ENSCJAG00000004494
• Aliases: None
• Description: RAD23 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:9812]

Sequence

>retro_cjac_3896
GGCCCCGCCATGGCTGTCACCATCACGCTCAAAACACTGCAGCAGCAGACCTTCAAGATCCTCATGGAGACCGACGAGAC
AGTGAGGGTACTAAAGGAGAAGATAGAAGCTGAGAAAGGTCGTGATGCTTTCCCCATGGCTGGACAGAAACTTATTTATG
CCAGCAAGATCTTGAGCGATGATGTCCGCATCAGGGGCTATCATATTGATGAGAAGAATTTTGTAATCATCATGGTGACC
AAGACCAAAGCTGGCCAGGGTACCTCAGCACCCCCAGAGGCCTCACCTACAGCTGCCCCAGAGTCCTCTACATCCTTCCC
GCCTGCCCCTACCTCAGGCATGTCCCACCCCCCACCTGCCGCCAGACAGGACAAGAGCCCGTGGGATGAATCCACCCCCA
CGACGTCCCCAGAGTCCGTGTCAGGCTCTGTTCCCTCTTCAGGTAGCAGCGGGCGAGAGGAAGATGCAGCCTCCACGCTA
GTGACGGGCTCTGAGTATGAGACGGTGATCACAGAGATCATGTCCATGGGCTATGAGCGGGAGCGGGTCCTGGCTGCCCT
GAGAGCCAGCTAAAACAACCCCCACTGAGCAGTGGAGTATATGCTCACGGGAATTCCTGGGAGCCCCGAGCCGGAACACG
ATTCTGTCCAGGAGAGCCAGGTATCTGAGCAGCTGGCCACGGAAGCAGCAGGAGAGAAACCCCTGGAGTTCCTGCGGGAC
CAGCCCCAGTTCTAGAACATGCGGCAGGTGATTCAGCAGAACCCTGCACTGCTGCCCGCTCTGCACCAACAGCTGGGCCA
GGAGAATCCTCAGCTTTTGCAGCAAATTAGCTGGCACCAGGAGCAGTTCATCCAGATGCTGAACGAACCCCCTGGAGAGC
TGGCAGACATCTCAGATGTGGAGGCAGAGGTGGGTGCCATAGGAGAGGAGGCCCGCCTATGAACTACATCCAGATGATGC
TGCAGGAGAAAGAAGCTATAGAGAGGTTGAAGGCCCTGGGGTTTCCAGAGAGCCTGGTTATCCAGGCCTATTTCGCGTGT
GAAAAAAACGAAAACTTGGCTGCCAACTTCCTCTTGAGTCAGAACTTTGATAATGAG

Alignment

ORF - retro_cjac_3896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.83 %
• Parental protein coverage: 96.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GPAMAVTITLKTLQQQTFKIRMEPKVEVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRID
          GPAMAVTITLKTLQQQTFKI.ME....V.VLKEKIEAEKGRDAFP.AGQKLIYA.KILSDDV.IR.Y.ID
Retrocopy GPAMAVTITLKTLQQQTFKILMETDETVRVLKEKIEAEKGRDAFPMAGQKLIYASKILSDDVRIRGYHID

Parental  EKNFVVVMVTKTKAGQGTSAPPEASPTAAPESSTSFLPAPTSGMSHPPPAAREDKSPSEESAPTTSPESV
          EKNFV..MVTKTKAGQG................TSF.PAPTSGMSHPPPAAR.DKSP..ES.PTTSPESV
Retrocopy EKNFVIIMVTKTKAGQGXXXXXXXXXXXXXXXXTSFPPAPTSGMSHPPPAARQDKSPWDESTPTTSPESV

Parental  SGSVPSSGSSGREEDAASTLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGIPGSPE
          SGSVPSSGSSGREEDAASTLVTGSEYET..TEIMSMGYERERV.AALRAS.NNPH.AVEY.LTGIPGSPE
Retrocopy SGSVPSSGSSGREEDAASTLVTGSEYETVITEIMSMGYERERVLAALRAS*NNPH*AVEYMLTGIPGSPE

Parental  PEHGSVQESQVSEQPATEAAGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQ
          PEH.SVQESQVSEQ.ATEAAGE.PLEFLRDQPQF.NMRQVIQQNPALLPAL.QQLGQENPQLLQQIS.HQ
Retrocopy PEHDSVQESQVSEQLATEAAGEKPLEFLRDQPQF*NMRQVIQQNPALLPALHQQLGQENPQLLQQISWHQ

Parental  EQFIQMLNEPPGELADISDVEAEVGAIGEEA-PQMNYIQVTPQEKEAIERLKALGFPESLVIQAYFACEK
          EQFIQMLNEPPGELADISDVEAEVGAIGEEA.P.MNYIQ...QEKEAIERLKALGFPESLVIQAYFACEK
Retrocopy EQFIQMLNEPPGELADISDVEAEVGAIGEEA<PPMNYIQMMLQEKEAIERLKALGFPESLVIQAYFACEK

Parental  NENLAANFLLSQNFDDE
          NENLAANFLLSQNFD.E
Retrocopy NENLAANFLLSQNFDNE

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	9.65 RPM
SRP051959_heart	0.00 RPM	19.43 RPM
SRP051959_kidney	0.04 RPM	16.77 RPM
SRP051959_liver	0.00 RPM	12.56 RPM
SRP051959_lung	0.00 RPM	16.28 RPM
SRP051959_lymph_node	0.00 RPM	14.29 RPM
SRP051959_skeletal_muscle	0.02 RPM	72.48 RPM
SRP051959_spleen	0.00 RPM	14.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3896 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3896 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3896 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004494	1 retrocopy	retro_cjac_3896 ,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,