RetrogeneDB ID: retro_cjac_415

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:75026200..75027753(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000000423
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARFGAP2
• Ensembl ID: ENSCJAG00000019965
• Aliases: None
• Description: None

Sequence

>retro_cjac_415
ATGGCGGCGGAACTGAGCAAGACCGAAATCCAGACTCTTTTTAAGAGGCTTCGTGCAGTTCCAACCAACAAGGCTTGTTT
CCATTGTAGTGCCAAGAATCCGAGTTGGGCCAGCATCACGTATGGTGTTTTCTTGTGCATTAACTGCTCTGGGGTGCACC
GCTCCCTGGGTGTCCACCTGAGCTTCATCAGGTCCACAGAGTTGGATTCCAACTGGAACTGGTTCCAGCTGAGGTGTATG
CAGGTCGGCGGGAATGCCAATGCAATGGCTTTTTTCCACCATCATGGATGCACGGCCAATGATGTCAACACCAAATACAA
TAGCCAAGCTGCCCAGATGTATGGGGAGAAGATCCAGCAGCTGGGGAGTACAGCCCTGGCTAGGCACGGCACTGATCTTT
GCATAGACAACATGAGTAGTGCTGTTCCTAGTCACTCCCCGGAGAAGGACTCTGATTTCTTCACAGAACACACTCAACCC
CCTTCCTGGGATGCACCAGCCACTGAGCCTTCAGGGACCCAGCAGCCAGCGTCATCTGCAGAAAGCAGTGGCCTGGCACA
GCCAGAGCATGGCCCCAACACAGACCTGCTTGGCACCTCACCCAAAGGCTCACTGGAACTGACAAGCTCCATCATTGGCA
AGAAGAAGCCAGCAGCAGCTAAGAAAGGGCTGGGTGCCAAGAAAGGCCTAGGGGCCCAGAAGGGGAGCAGCCAGAGCTTC
AACGAGATTGAACGGCAGGCCCAGGTGGCAGAGAAGCTCCGAGAGCAGCAGGCAGCCGATGCCAGGAAGCAGGCGGAGGA
GTCCATGGTCGCCTCCATGCGTCTGGCCTATCCGGAGCTCCAGATTGATCGTAAGAAAGAGGAAAAGAAGCTACAGAATC
TGGAAGGGAAGAAGCGAGAGCAAGCAAAGAGGCAGGCATGGGCTTGGTATCTTGAAGCTCTGTCTCCCACTCCGTGCTGT
CTGAGATGCAGGTGATCGAGCAGGAAACCCCAGTGAGTGCGAAATCTCACTCGCAGCTGGACTTGTTTGATGATGTTGGT
ACTTTCGCCTCTGGACCCCCCAAGTACAAGGACAACCCCTTTTCCTTAGGAGAAAGCTTTGGTTCCCGCTGGGCTACAGA
TGCTGCCTGGGGTATGGAGAGGGTAGAGAATGAGCCAGAAGTGACCGTCTCAAGCATCCGGCCTATTTCAGAAAGGGCCA
CAAACCGGAGGGAGGTGGAGAGCCGGAGCACAGGCCTCGAGTCTAGTGAAGCGCGTCAGAAATTCGCAGGAGCCAAAGCC
ATCTCATCTGACATGTCCTTTGGGTGGGAGGTGGATGCGGAGTATGAGGCTAGGTCTCGGCTGCAGCAGCTCTCAGGCAG
CAGTGCCATCAGCTCTTCAGACCTCTTTGGGGACATAGACGGAGCTCATGAAGCAGGAAGTGTATCTCTCAGGAACGTGC
TGCCTACAGCGGACATTGCTCAGTTTAAGCAGGGTGTCAAGTCTGTGGCCGGGAAGATGGCTGTGCTTGCCAATGGTGTG
ATGAATTCCTTGCAGGATCGCTACGGTTCCTAC

Alignment

ORF - retro_cjac_415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAEPSKTEIQTLFKRLRAVPTNKACFDCGAKNPSWASITYGVFLCIDCSGVHRSLGVHLSFIRSTELDS
          MAAE.SKTEIQTLFKRLRAVPTNKACF.C.AKNPSWASITYGVFLCI.CSGVHRSLGVHLSFIRSTELDS
Retrocopy MAAELSKTEIQTLFKRLRAVPTNKACFHCSAKNPSWASITYGVFLCINCSGVHRSLGVHLSFIRSTELDS

Parental  NWNWFQLRCMQVGGNANATAFFRQHGCTASDANTKYNSRAAQMYREKIRQLGSAALARHGTDLWIDNMSS
          NWNWFQLRCMQVGGNANA.AFF..HGCTA.D.NTKYNS.AAQMY.EKI.QLGS.ALARHGTDL.IDNMSS
Retrocopy NWNWFQLRCMQVGGNANAMAFFHHHGCTANDVNTKYNSQAAQMYGEKIQQLGSTALARHGTDLCIDNMSS

Parental  AVPSHSPEKKDSDFFTEHTQPPSWDAPATEPSGTQQPASSSESSGLAQPEHGPNTDLLGTSPKASLELKS
          AVPSHSPEK.DSDFFTEHTQPPSWDAPATEPSGTQQPASS.ESSGLAQPEHGPNTDLLGTSPK.SLEL.S
Retrocopy AVPSHSPEK-DSDFFTEHTQPPSWDAPATEPSGTQQPASSAESSGLAQPEHGPNTDLLGTSPKGSLELTS

Parental  SIIGKKKPATAKKGLGAKKGLGAQKVSSQSFNEIERQAQVAEKLREQQAADAKRQAEESMVASMRLAYQE
          SIIGKKKPA.A...............SSQSFNEIERQAQVAEKLREQQAADA..QAEESMVASMRLAY.E
Retrocopy SIIGKKKPAAAXXXXXXXXXXXXXXXSSQSFNEIERQAQVAEKLREQQAADARKQAEESMVASMRLAYPE

Parental  LQIDRKKEEKKLQNLEGKKREQAER-LGMGLVSRSSVSHSVLSEMQVIEQETPVSAKSSRSQLDLFDDVG
          LQIDRKKEEKKLQNLEGKKREQA.R..GMGLVS.SSVSHSVLSEMQVIEQETPVSAKS..SQLDLFDDVG
Retrocopy LQIDRKKEEKKLQNLEGKKREQAKR<AGMGLVS*SSVSHSVLSEMQVIEQETPVSAKS-HSQLDLFDDVG

Parental  TFASGPPKYKDNPFSLGESFGSRWDTDATWGVDRVEKEPEVTVSSIRPISERATNRREVESRSTGLESSE
          TFASGPPKYKDNPFSLGESFGSRW.TDA.WG..RVE.EPEVTVSSIRPISERATNRREVESRSTGLESSE
Retrocopy TFASGPPKYKDNPFSLGESFGSRWATDAAWGMERVENEPEVTVSSIRPISERATNRREVESRSTGLESSE

Parental  ARQKFAGAKAISSDMFFGREVDAEYEARSRLQQLSGSSAISSSDLFGDMDGAHGAGSVSLGNVLPTADIA
          ARQKFAGAKAISSDM.FG.EVDAEYEARSRLQQLSGSSAISSSDLFGD.DGAH.AGSVSL.NVLPTADIA
Retrocopy ARQKFAGAKAISSDMSFGWEVDAEYEARSRLQQLSGSSAISSSDLFGDIDGAHEAGSVSLRNVLPTADIA

Parental  QFKQGVKSVAGKMAVLANGVMNSLQDRYGSY
          QFKQGVKSVAGKMAVLANGVMNSLQDRYGSY
Retrocopy QFKQGVKSVAGKMAVLANGVMNSLQDRYGSY

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	19.13 RPM
SRP051959_heart	0.02 RPM	31.27 RPM
SRP051959_kidney	0.02 RPM	29.73 RPM
SRP051959_liver	0.02 RPM	27.77 RPM
SRP051959_lung	0.03 RPM	27.93 RPM
SRP051959_lymph_node	0.00 RPM	26.67 RPM
SRP051959_skeletal_muscle	0.04 RPM	46.54 RPM
SRP051959_spleen	0.02 RPM	25.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_415 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_415 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_415 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	ENSCJAG00000019965	1 retrocopy	retro_cjac_415 ,
Macropus eugenii	ENSMEUG00000004984	1 retrocopy	retro_meug_1841,
Microcebus murinus	ENSMICG00000007019	1 retrocopy	retro_mmur_51,
Mus musculus	ENSMUSG00000027255	1 retrocopy	retro_mmus_2776,
Oryctolagus cuniculus	ENSOCUG00000002073	2 retrocopies	retro_ocun_1769, retro_ocun_599,