RetrogeneDB ID: retro_cjac_4049

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:26569652..26570132(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000018958
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000003097
• Aliases: None
• Description: None

Sequence

>retro_cjac_4049
GTGGGCAGCACCTGGGGGAGCCCTGGCTGGGTGCAGCTCATGCTCTTCCTGGCTGACTTAGTGCTCTGGTTCTATGCACT
GCACGTGAAGGCGGCGCGCCCATGGGACCCATATTACCACGCGCTCTGCAACGTGGGCACCGCCATCAGCTGTTCACGTA
TTTTCTCCAGGTGGGGCATGGGCCTCAGGCTGGTGGAGCAGGTGCTGGGAAAGGGCAGCATCCTCAATCAATCCAATAGC
ATATTCCGTTGCATCTTCTACATGCCACAGCTGTTGTTAGGTTGCCTGAGGACACTCTGGGCCTCTGTCCTGCTGCTGCT
GAGATCCCCGGTGTCTCTCACTGATTCAGTCTACCTGGCCTGGACGCTGTTCTTCATGCTCTATGATTTCTGCATCATTT
GCATCACTACCTATGCCATCAACGTGGGTCTGATGTGGCTTAGTTTCTGGAAGGTCCAAGAACCCCAGAGCAAGGCTGAG

Alignment

ORF - retro_cjac_4049 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.91 %
• Parental protein coverage: 98.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGSTWGNPGWVRLALCLVGLVLSLYALHVKAARARDRDYRALCDVGTAISCSRVFSSRWGRGFGLVEHVL
          .GSTWG.PGWV.L.L.L..LVL..YALHVKAAR..D..Y.ALC.VGTAISCSR.FS.RWG.G..LVE.VL
Retrocopy VGSTWGSPGWVQLMLFLADLVLWFYALHVKAARPWDPYYHALCNVGTAISCSRIFS-RWGMGLRLVEQVL

Parental  GQDSILNQSNSIFGCIFYTLQLLLGCLQTRWAALLLLLSSLVSLAGSVYLAWILFFVLYDFCIVCITTYA
          G..SILNQSNSIF.CIFY..QLLLGCL.T.WA..LLLL.S.VSL..SVYLAW.LFF.LYDFCI.CITTYA
Retrocopy GKGSILNQSNSIFRCIFYMPQLLLGCLRTLWASVLLLLRSPVSLTDSVYLAWTLFFMLYDFCIICITTYA

Parental  INMGLMWLSFQKIQEPQGKAK
          IN.GLMWLSF.K.QEPQ.KA.
Retrocopy INVGLMWLSFWKVQEPQSKAE

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	4.02 RPM
SRP051959_heart	0.00 RPM	5.77 RPM
SRP051959_kidney	0.00 RPM	11.34 RPM
SRP051959_liver	0.00 RPM	97.86 RPM
SRP051959_lung	0.00 RPM	5.34 RPM
SRP051959_lymph_node	0.00 RPM	3.95 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.67 RPM
SRP051959_spleen	0.00 RPM	6.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4049 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4049 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4049 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3624

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003097	1 retrocopy	retro_cjac_4049 ,
Homo sapiens	ENSG00000167397	1 retrocopy	retro_hsap_4664,
Oryctolagus cuniculus	ENSOCUG00000002289	1 retrocopy	retro_ocun_1423,
Ochotona princeps	ENSOPRG00000016146	3 retrocopies	retro_opri_1124, retro_opri_1164, retro_opri_70,
Pongo abelii	ENSPPYG00000007306	1 retrocopy	retro_pabe_3624,
Pan troglodytes	ENSPTRG00000008031	1 retrocopy	retro_ptro_3099,