RetrogeneDB ID: retro_cjac_1759

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:411580..412386(+)
• Located in intron of: ENSCJAG00000010221

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRA2A
• Ensembl ID: ENSCJAG00000001509
• Aliases: None
• Description: None

Sequence

>retro_cjac_1759
GAGTCTCGCTCTCAGTCAAAATCTCCAACGGGAACTCCTGCTCGTGTAAAATTGGAGAGCAGGTCAGGATCTCGTAGTCC
ATCCAGGGTTTCCAAACACTCTGAATCCCATTCTCGATCAAGATCAAAATCCAGGTCAAGGTCAAGGAGACATTCTCATA
GACGTTATACTCGATCCAGATCCCACTCTCACTCTCATAGGAGACGATCTCGAAGTAGATCATATACACCAGAATACCGG
CGGCGAAGGAGCCGAAGCCATTCTCCAATGTCTAACCGGAGAAGACATACTGGCAGCAGGGCAAACCCAGATCCCAACAC
TTGCCTTGGAGTGTTTGGCCTCAGTTTGTACATAACAGAGAGAGATCTTCGTGAAGTATTTTCTCGATATGGACCATTGA
GTGGTGTCAATGTGGTTTATGATCAGCGAACGGGGCGATCTCGAGGATTGCTTTTGTATATTTTGAGCGAATAGATGACT
CAAAGGAGGCTATGGAAAGAGCAAATGGAATGGAGCTGGATGGTAGAAGAATTCGAGTGGATTATTCTATCACCAAGAGA
GCGCACACACCTACACCAGACATCTACATGGGCAGACCAACCCATGGTGGTGGTGGTGGAGGAGGCGGTGGCGGTGGAGG
TGGAGGTGGTGGCAGACGTCGAGATTCTTACTATGATAGAGGTTATGATCGTGGGTATGACAGATATGAAGACTATGATT
ACCGGTACAGAAGACGATCACCTTCTCCTTATTAAAGTCGATACAGATCACGATCACGATCTCGTTCCTACAGCCCAAGA
CGCTAC

Alignment

ORF - retro_cjac_1759 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.19 %
• Parental protein coverage: 95.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESRSQSKSPTGTPARVKSESRSGSRSPSRVSKHSESHSRSRSKSRDRIKVHSHRRYTRSRSHSHSHRRRS
          ESRSQSKSPTGTPARVK.ESRSGSRSPSRVSKHSESHSRSRSKSR.R...HSHRRYTRSRSHSHSHRRRS
Retrocopy ESRSQSKSPTGTPARVKLESRSGSRSPSRVSKHSESHSRSRSKSRSRSRRHSHRRYTRSRSHSHSHRRRS

Parental  RSRSYTPEYRRRRSRSHSPMSNRRRHTGSRANPDPNTCLGVFGLSLYTTERDLREVFSRYGPLSGVNVVY
          RSRSYTPEYRRRRSRSHSPMSNRRRHTGSRANPDPNTCLGVFGLSLY.TERDLREVFSRYGPLSGVNVVY
Retrocopy RSRSYTPEYRRRRSRSHSPMSNRRRHTGSRANPDPNTCLGVFGLSLYITERDLREVFSRYGPLSGVNVVY

Parental  DQRTGRSRG-FAFVYFERIDDSKEAMERANGMELDGRRIRVDYSITKRAHTPTPGIYMGRPTQRENFFPV
          DQRTGRSRG..AFVYFERIDDSKEAMERANGMELDGRRIRVDYSITKRAHTPTP.IYMGRPT........
Retrocopy DQRTGRSRG<IAFVYFERIDDSKEAMERANGMELDGRRIRVDYSITKRAHTPTPDIYMGRPTXXXXXXXX

Parental  FKIDFGKVGGRRRDSYYDRGYDRGYDRYEDYDYRYRRRSPSPYYSRYRSRSRSRSYSPRRY
          ..........RR...Y.DRGYDRGYDRYEDYDYRYRRRSPSPY.SRYRSRSRSRSYSPRRY
Retrocopy XXXXXXXXXRRRDSYY-DRGYDRGYDRYEDYDYRYRRRSPSPY*SRYRSRSRSRSYSPRRY

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	2.11 RPM	14.47 RPM
SRP051959_heart	2.10 RPM	16.26 RPM
SRP051959_kidney	2.93 RPM	18.21 RPM
SRP051959_liver	2.36 RPM	13.19 RPM
SRP051959_lung	4.38 RPM	24.87 RPM
SRP051959_lymph_node	4.93 RPM	29.86 RPM
SRP051959_skeletal_muscle	2.60 RPM	15.02 RPM
SRP051959_spleen	4.16 RPM	27.65 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1759 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1759 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1759 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001130	1 retrocopy	retro_chof_974,
Callithrix jacchus	ENSCJAG00000001509	1 retrocopy	retro_cjac_1759 ,
Echinops telfairi	ENSETEG00000007250	2 retrocopies	retro_etel_323, retro_etel_692,
Homo sapiens	ENSG00000164548	1 retrocopy	retro_hsap_386,
Gorilla gorilla	ENSGGOG00000009053	1 retrocopy	retro_ggor_391,
Mustela putorius furo	ENSMPUG00000013480	1 retrocopy	retro_mputfur_1442,
Nomascus leucogenys	ENSNLEG00000014794	1 retrocopy	retro_nleu_1481,
Otolemur garnettii	ENSOGAG00000009733	3 retrocopies	retro_ogar_1966, retro_ogar_2558, retro_ogar_3027,
Pongo abelii	ENSPPYG00000017728	1 retrocopy	retro_pabe_324,
Pan troglodytes	ENSPTRG00000018988	1 retrocopy	retro_ptro_299,
Sorex araneus	ENSSARG00000012900	1 retrocopy	retro_sara_467,