RetrogeneDB ID: retro_cjac_459

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:121466964..121467964(+)
• Located in intron of: ENSCJAG00000009094

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPG
• Ensembl ID: ENSCJAG00000019705
• Aliases: None
• Description: capping protein (actin filament), gelsolin-like [Source:HGNC Symbol;Acc:1474]

Sequence

>retro_cjac_459
TACGCAGCCATTCCCCAGAGTGGCTCTCCATTTTCAGCCTCAGTGTGGGATCCAGGCCTGCATATGTGGAGGGTGGAGAA
GCTGAAGCCAGTGCCTGTGGCGTGAGAGAACCAGGGCGTCTCCTCGGGGACTTCTACCTACTGCTGTACAATGGCCCAGA
AGAGGTTTCCCATCTGCACCTGTGGATAGGCCAGCAGTCATCCTGGCATGAGCGGGGGTCCTGTGCTGTGCTGGCTGTGC
ACCTCAACACACTGCTGGGAGAGCGGCCTGTGCAGCACCGTGAGGTGCAGGGCAGTGAGTCCAATCTCTTCATGAGCTAC
TTCCCACAGGGCCTCAAGTACCAGGAAGGTGGTGTGGAGTCAGCATTTCACAAGACCTCCTCAGGAGGCCCAGCTGCCGT
CAAGAAACTCTACCAGGTGAAGGGGAGAAGAACATCCATGCCACTGAGTGGGCAGTGAGCTGGGACAGCTTCAACATGGG
GGACTGCTTCATCCTGGACCTGGGCCAGAACATCTTTGCCTGATGTGGTGGAAAGTCCAACATCCTGGAACGCAGCAAGG
CGAGAGACCTGGCCCTGGCCATCCGGGACAGTGAGCGACAGGGCAAGGCCCAGGTGGAGATTGTCACTGATGGGGAGGAG
CCTTATGAGATGATCCAGGTTCTGGGCCCCAAGCCTTCTCTCAAGGAGGGCAACCCCGAGGAAGACCTCACAGCTGACCA
GACAAATGCCCAGGCCATGGCTCTGTATAAGGTCTCTGATGTCACTGGACAGATGAACCTGACCAAGGTGGCTGACTCCA
GTCCCTTTTTCCCCGAACTGCTGATGTCTGATGACTGCTCTGTGCTGGACAATGGGCTCTGTGGCAAGATCTATATCTGG
AAGGGACGAAAAGCGAATGAGAAGGAGCGGCAGGCAAACCTGCAAGTGGCTGAGGGCTTCATCTTGCACATGTGGTATGC
CCTCAACACTCAGGTGGAGATATTGCCCCAGGGCCGTGAG

Alignment

ORF - retro_cjac_459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.54 %
• Parental protein coverage: 96.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YTAIPQSGSPFSASVQDPGLHVWRVEKLKPVPVARENQGVFFSG-DSYLVLHNGPEEVSHLHLWIGQQSS
          Y.AIPQSGSPFSASV.DPGLH.WRVEKLKPVPVA.ENQGV..SG.D.YL.L.NGPEEVSHLHLWIGQQSS
Retrocopy YAAIPQSGSPFSASVWDPGLHMWRVEKLKPVPVA*ENQGV-SSG<DFYLLLYNGPEEVSHLHLWIGQQSS

Parental  RDEQGACAVLAVHLNTLLGERPVQHREVQGNESDLFMSYFPRGLKYQEGGVESAFHKTSSGAPAAIKKLY
          ..E.G.CAVLAVHLNTLLGERPVQHREVQG.ES.LFMSYFP.GLKYQEGGVESAFHKTSSG.PAA.KKLY
Retrocopy WHERGSCAVLAVHLNTLLGERPVQHREVQGSESNLFMSYFPQGLKYQEGGVESAFHKTSSGGPAAVKKLY

Parental  QVKGK-KNIRATERALSWDSFNTGDCFILDLGQNIFAWCGGKSNILERNKARDLALAIRDSERQGKAQVE
          QVKG..KNI.ATE.A.SWDSFN.GDCFILDLGQNIFA.CGGKSNILER.KARDLALAIRDSERQGKAQVE
Retrocopy QVKGR<KNIHATEWAVSWDSFNMGDCFILDLGQNIFA*CGGKSNILERSKARDLALAIRDSERQGKAQVE

Parental  IVTDGEEPAEMIQVLGPK-ALKEGNPEEDLTADQTNSQAAALYKVSDATGQMNLTKVADSSPFALELLIS
          IVTDGEEP.EMIQVLGPK..LKEGNPEEDLTADQTN.QA.ALYKVSD.TGQMNLTKVADSSPF..ELL.S
Retrocopy IVTDGEEPYEMIQVLGPKPSLKEGNPEEDLTADQTNAQAMALYKVSDVTGQMNLTKVADSSPFFPELLMS

Parental  DDCFVLDNGLCGKIYIWKGRKANEKERQAALQVAEGFISRMRYAPNTQVEILPQGRE
          DDC.VLDNGLCGKIYIWKGRKANEKERQA.LQVAEGFI..M.YA.NTQVEILPQGRE
Retrocopy DDCSVLDNGLCGKIYIWKGRKANEKERQANLQVAEGFILHMWYALNTQVEILPQGRE

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	2.42 RPM	36.70 RPM
SRP051959_heart	1.67 RPM	5.40 RPM
SRP051959_kidney	1.38 RPM	6.32 RPM
SRP051959_liver	1.13 RPM	5.18 RPM
SRP051959_lung	2.68 RPM	14.82 RPM
SRP051959_lymph_node	3.45 RPM	14.31 RPM
SRP051959_skeletal_muscle	1.48 RPM	2.36 RPM
SRP051959_spleen	2.69 RPM	45.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_459 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_459 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_459 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019705	2 retrocopies	retro_cjac_3816, retro_cjac_459 ,
Macropus eugenii	ENSMEUG00000013559	1 retrocopy	retro_meug_1063,
Mus musculus	ENSMUSG00000056737	1 retrocopy	retro_mmus_3506,
Otolemur garnettii	ENSOGAG00000001084	1 retrocopy	retro_ogar_3277,
Rattus norvegicus	ENSRNOG00000013668	1 retrocopy	retro_rnor_840,