RetrogeneDB ID: retro_cjac_3952

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286408.1:1735..2381(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19orf40
• Ensembl ID: ENSCJAG00000000728
• Aliases: None
• Description: chromosome 19 open reading frame 40 [Source:HGNC Symbol;Acc:28467]

Sequence

>retro_cjac_3952
ATGGAAAGGAACCCCCCCTGATGGCATGGGCCCCATGCACGTGCCTTTGGGGCATGTTGTAGCCAATGAGAAATGGTGTG
GGTCACAGCTGGTGCAGGAAATGCAAGGGAAAATTAAGCTCATTTTCGAGGATGGCTTGACACCAGACTTTTAACTGTTG
AACAGATGGTATGTTCTTTATGTCACTGAAGCTGATTTGGTGACAGGAAATGGCTACAGAAAGAGGCTCATTCAGGTTAG
AAATTCCAGTAATCTTCAAGGAGTTATAGTTGTTGAAAAAATCTAGATGAGTGAACAATAATTCCCAGCCTTACAGAAGT
TTACTGTTCTGAATCTTTGAATGATGCTGCTTCCAGTGGCCAGCCAGATTGAAGCATCCTGCCTCGTCATCCAGTCGGTT
CAAGAGCAAACTATAGAGGCCAGTAAGAACTCTCTTCTTAGGAAGAAACAAGCTCTGCTGCTGTCTGAGCCATCACTCCT
TTGAAGCATGCAGCAGATCCCAGGAGTTGAAAAGGTTAAAGCTCCGCTTCTGCTCCAGAAATTTCCAAGCATTCAGCAAC
TGAGTAATGTTTCCATTCAGGAACTGGAGCAGGTGGTCAGACAAGCAGTAGCACAGCAGATCCATGCCTTCTTCACACAG
CCCAGG

Alignment

ORF - retro_cjac_3952 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MERNPS-DGTGPVHVPLGQVVANEKWRGSQLAQEMQGKIKLIFEDGLTPDFYLSNRCCILYVTEADLVAG
          MERNP..DG.GP.HVPLG.VVANEKW.GSQL.QEMQGKIKLIFEDGLTPDF.L.NR...LYVTEADLV.G
Retrocopy MERNPP>DGMGPMHVPLGHVVANEKWCGSQLVQEMQGKIKLIFEDGLTPDF*LLNRWYVLYVTEADLVTG

Parental  NGYRKRLVRVRNSNNIQGIVVVEKTQMSEQYFPALQKFTVLDLGMVLLPVANQMEASCLIIQLVQEQIKE
          NGYRKRL..VRNS.N.QG..VVEK..MSEQ.FPALQKFTVL.L.M.LLPVA.Q.EASCL.IQ.VQEQ..E
Retrocopy NGYRKRLIQVRNSSNLQGVIVVEKI*MSEQ*FPALQKFTVLNL*MMLLPVASQIEASCLVIQSVQEQTIE

Parental  PSKNPLLGKKRALLLSEPSLLRTVQQIPGVGKVKAPLLLQKFPSIQKLSNASIRELEQVVGQAVAQQIHA
          .SKN.LL.KK.ALLLSEPSLL...QQIPGV.KVKAPLLLQKFPSIQ.LSN.SI.ELEQVV.QAVAQQIHA
Retrocopy ASKNSLLRKKQALLLSEPSLL*SMQQIPGVEKVKAPLLLQKFPSIQQLSNVSIQELEQVVRQAVAQQIHA

Parental  FFTQPR
          FFTQPR
Retrocopy FFTQPR

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	1.13 RPM
SRP051959_heart	0.00 RPM	0.79 RPM
SRP051959_kidney	0.00 RPM	1.97 RPM
SRP051959_liver	0.00 RPM	1.13 RPM
SRP051959_lung	0.02 RPM	1.37 RPM
SRP051959_lymph_node	0.00 RPM	1.62 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.15 RPM
SRP051959_spleen	0.00 RPM	1.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3952 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3952 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3952 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000728	2 retrocopies	retro_cjac_1011, retro_cjac_3952 ,
Cavia porcellus	ENSCPOG00000011965	1 retrocopy	retro_cpor_1536,
Dasypus novemcinctus	ENSDNOG00000014134	4 retrocopies	retro_dnov_1817, retro_dnov_2382, retro_dnov_426, retro_dnov_942,
Echinops telfairi	ENSETEG00000002716	1 retrocopy	retro_etel_458,
Loxodonta africana	ENSLAFG00000006401	4 retrocopies	retro_lafr_165, retro_lafr_365, retro_lafr_415, retro_lafr_789,
Myotis lucifugus	ENSMLUG00000013287	1 retrocopy	retro_mluc_522,
Macaca mulatta	ENSMMUG00000017939	1 retrocopy	retro_mmul_788,
Procavia capensis	ENSPCAG00000009727	1 retrocopy	retro_pcap_444,
Sarcophilus harrisii	ENSSHAG00000016372	1 retrocopy	retro_shar_299,