RetrogeneDB ID: retro_cjac_3159

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:100081660..100082467(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DAP3
• Ensembl ID: ENSCJAG00000008125
• Aliases: None
• Description: None

Sequence

>retro_cjac_3159
ACACTACTGAAAGGAATAATAAGGCTTATCTCTAGGATCCATAAGTTGGACCCTGGGCTTTTGTTACACATGGGAACCCA
GGCACACCAAAGCATTGCTGCTCACCTAGATAACCAGGTTCCAGTTGAGAGTCCCAGAGCTATTTCCCACACCAATGAGA
ATGACCCAGCTAAGCATGGGGATCAGCATGAGGGTCAGCACTACAACATCTTCCCCCAGGATATGAAGACAGTAGTTCCC
CAGGGCCTTCCTCCTCGCTTTGTGATGCAGGTGAAGACATTCAGTGAAGCTTACCTGATGGAAAGGAAACCAGCCCTGGA
ACTTCTGCATTACCTGAAAAAACACCAATGTTGCTTATCCGACTGTATGATATCTTCTGTATGGGGAGAAGGGAACAGGA
AAAACTCTCAGTCTTTGCCATATTATTAATTTCTGTGCAAAACAGGACTGGATGATACTACATATTCCAGATGCTCATAA
TGGGGTAAAAAATTTCCGGGAACTTCTACAGTCGAACTACAACAAACAACTCTTTGATCAACCTTTAGAGGCTTCAACCT
GGCTGAAGAATTTCAAAACTACAAGTGATTGCTTCCTGAACCAGATAAAAATTCAAGAGAAGTATGTCTGGAATAAGAGA
GGAAGCACTGAGAAAGGCAGTCCTCTGGGAGAAGTGGTTGAACAGGGCATAACACAGGTGAGGAACGCCTCAGATGCATT
GGAATTGTGCTGAAAGAGCTAAAGAGGCAAAGTTCTTTGGGTATTTTTCACCTCCTGGTGGCCGTGGATAGAATAAAAGG
CACTTGG

Alignment

ORF - retro_cjac_3159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.24 %
• Parental protein coverage: 67.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TMLKGITRLISKIRKLDPGRSLHVGTQAHQSIAAHLDNQVPVGSPRAISRTNENDPAKHGDQHEGQHYNI
          T.LKGI.RLIS.I.KLDPG..LH.GTQAHQSIAAHLDNQVPV.SPRAIS.TNENDPAKHGDQHEGQHYNI
Retrocopy TLLKGIIRLISRIHKLDPGLLLHMGTQAHQSIAAHLDNQVPVESPRAISHTNENDPAKHGDQHEGQHYNI

Parental  SPQDLKTVFPHGLPPRFVMQVKTFSEAYLMVRKPALELLHYLK-NTNFSYPAVRYLLYGEKGTGKTLSLC
          .PQD.KTV.P.GLPPRFVMQVKTFSEAYLM.RKPALELLHYLK.NTN..YP.V.YLLYGEKGTGKTLSLC
Retrocopy FPQDMKTVVPQGLPPRFVMQVKTFSEAYLMERKPALELLHYLK>NTNVAYPTV*YLLYGEKGTGKTLSLC

Parental  HVIHFCAKQDWLILHIPDAHLWVKNCRELLQSNYNKQRFDQPLEASSWLKNFKTTNERFLNQIKVQEKYV
          H.I.FCAKQDW.ILHIPDAH..VKN.RELLQSNYNKQ.FDQPLEAS.WLKNFKTT...FLNQIK.QEKYV
Retrocopy HIINFCAKQDWMILHIPDAHNGVKNFRELLQSNYNKQLFDQPLEASTWLKNFKTTSDCFLNQIKIQEKYV

Parental  WNKRESTEKGSPLGEVVEQGITRVRNATDA-VGIVLKELKRQSSLGIFHLLVAVDGINAVW
          WNKR.STEKGSPLGEVVEQGIT.VRNA.DA..GIVLKELKRQSSLGIFHLLVAVD.I...W
Retrocopy WNKRGSTEKGSPLGEVVEQGITQVRNASDA<IGIVLKELKRQSSLGIFHLLVAVDRIKGTW

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	0.04 RPM	13.09 RPM
SRP051959_heart	0.12 RPM	15.65 RPM
SRP051959_kidney	0.04 RPM	17.62 RPM
SRP051959_liver	0.00 RPM	17.57 RPM
SRP051959_lung	0.03 RPM	18.27 RPM
SRP051959_lymph_node	0.02 RPM	22.81 RPM
SRP051959_skeletal_muscle	0.00 RPM	18.13 RPM
SRP051959_spleen	0.00 RPM	22.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3159 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3159 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3159 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008125	1 retrocopy	retro_cjac_3159 ,
Macropus eugenii	ENSMEUG00000015501	1 retrocopy	retro_meug_958,