RetrogeneDB ID: retro_cjac_3078

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:65237164..65238010(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032875
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000017810
• Aliases: None
• Description: None

Sequence

>retro_cjac_3078
GTAGTCATTTCTGGAAGGAAACTGGCCCAGCGGATCAAGCAGGAAGTCTGGCAGGAGGTGAGAGAGTGGATGTAATTCCT
GTAACAGATGACCACACCTGAGCGTGATCCGGGTCAGCGAGAATTTTGCAAGTCACTCCTATATCCTCAACAAAACCAGG
GCAGCTGAAGAAGTGGGAATCAACAGTGAGACAATTGTGAAACCAGCTTCAATTTCAGAGGAAGAATTGTTGAGTTTACT
CAATAAACTGAATAATAATGATAATGTAGATGGCCTCCTTGTTCAGCTGCCTCTTCCAGAGCATATTAATAAGAGAAAGA
TCTGCAATGCTGTTTCTCCAGACAAGGATGTTGACGGCTTCCCCGTCGTTAATGTAGGGCGAATATGTTTGGATCAGTAT
TCCATGTTATGGGCTACCCCATGGGAAATAATTAAGTGAACTGGCATTCCTACCCTAGGGAAGAATGTGGTTGTGGCTGG
AAGGTCAAAAAATGTTGGAATGCACATTGCAATATTACTGCACACAGAGCGGGTCCATGAAGGTCCCGAGGGTGATGCCA
CTGTTACAATATCTCATCAATATACTCCCAACGAGCCACTGAAGAAACATACTATTCTTGCAGATATTCTAATATCTGCT
GCCAGCATTCCAAATCTGATCACAGTAGATATCATCAAGGAAGGAGCAGCACTCATTGATCTGGGAATAAATAGAGTTCA
CAGTCCCATAACTGTCAAACCTAATTGGTTGGAGATGAGGATTTTGAAGGAGTAAGACAAAAAGCTGGTTATATCACTCC
AGTTCCTGGAGGTGTTGGCCCAGTAGCAGCGACGATGCAAAAAAAA

Alignment

ORF - retro_cjac_3078 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.14 %
• Parental protein coverage: 81.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVISGRKLAQQIKQEVRQEVEEWV-ASGNKQPHLSVILVGENPASHSYVLNKTRAAADVGINSETIVKSA
          VVISGRKLAQ.IKQEV.QEV.EW...S.N..PHLSVI.V.EN.ASHSY.LNKTRAA..VGINSETIVK.A
Retrocopy VVISGRKLAQRIKQEVWQEVREWM>NSCNR*PHLSVIRVSENFASHSYILNKTRAAEEVGINSETIVKPA

Parental  SISEEELLNLINKLNNDDNVDGLLVQLPLPEHIDERKICNAVSPDKDVDGFHVINVGRMCLDQYSMLPAT
          SISEEELL.L.NKLNN.DNVDGLLVQLPLPEHI..RKICNAVSPDKDVDGF.V.NVGR.CLDQYSML.AT
Retrocopy SISEEELLSLLNKLNNNDNVDGLLVQLPLPEHINKRKICNAVSPDKDVDGFPVVNVGRICLDQYSMLWAT

Parental  PWGVWEIIKRTGIPTLGKNVVVAGRSKNVGMPIAMLLHTDGAHERPGGDATVTISHRYTPKEQLKKHTIL
          PW...EIIK.TGIPTLGKNVVVAGRSKNVGM.IA.LLHT...HE.P.GDATVTISH.YTP.E.LKKHTIL
Retrocopy PW---EIIK*TGIPTLGKNVVVAGRSKNVGMHIAILLHTERVHEGPEGDATVTISHQYTPNEPLKKHTIL

Parental  ADIVISAAGIPNLITADMIKEGAAVIDVGINRVHDPVTAKPK-LVGDVDFEGVRQKAGYITPVPGGVGPM
          ADI.ISAA.IPNLIT.D.IKEGAA.ID.GINRVH.P.T.KP..LVGD.DFEGVRQKAGYITPVPGGVGP.
Retrocopy ADILISAASIPNLITVDIIKEGAALIDLGINRVHSPITVKPN<LVGDEDFEGVRQKAGYITPVPGGVGPV

Parental  TVAMLMK
          ...M..K
Retrocopy AATMQKK

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	54.49 RPM
SRP051959_heart	0.02 RPM	18.86 RPM
SRP051959_kidney	0.00 RPM	29.91 RPM
SRP051959_liver	0.04 RPM	8.08 RPM
SRP051959_lung	0.00 RPM	23.62 RPM
SRP051959_lymph_node	0.00 RPM	29.09 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.38 RPM
SRP051959_spleen	0.44 RPM	41.39 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3078 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3078 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3078 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2641

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017345	2 retrocopies	retro_amel_1098, retro_amel_1584,
Canis familiaris	ENSCAFG00000008716	1 retrocopy	retro_cfam_580,
Callithrix jacchus	ENSCJAG00000013883	1 retrocopy	retro_cjac_1764,
Callithrix jacchus	ENSCJAG00000017810	3 retrocopies	retro_cjac_2225, retro_cjac_2568, retro_cjac_3078 ,
Homo sapiens	ENSG00000065911	5 retrocopies	retro_hsap_2732, retro_hsap_2817, retro_hsap_3002, retro_hsap_3309, retro_hsap_3874,
Macropus eugenii	ENSMEUG00000013987	4 retrocopies	retro_meug_1468, retro_meug_152, retro_meug_1577, retro_meug_2074,
Mustela putorius furo	ENSMPUG00000007829	3 retrocopies	retro_mputfur_1087, retro_mputfur_1397, retro_mputfur_1551,
Nomascus leucogenys	ENSNLEG00000000326	5 retrocopies	retro_nleu_1196, retro_nleu_207, retro_nleu_2501, retro_nleu_595, retro_nleu_749,
Otolemur garnettii	ENSOGAG00000009089	1 retrocopy	retro_ogar_3390,
Pongo abelii	ENSPPYG00000012283	3 retrocopies	retro_pabe_2271, retro_pabe_2729, retro_pabe_3077,
Pan troglodytes	ENSPTRG00000012081	4 retrocopies	retro_ptro_1846, retro_ptro_1910, retro_ptro_2162, retro_ptro_2641,
Pteropus vampyrus	ENSPVAG00000013948	2 retrocopies	retro_pvam_1357, retro_pvam_1414,
Rattus norvegicus	ENSRNOG00000010833	1 retrocopy	retro_rnor_2170,