RetrogeneDB ID: retro_cjac_1229

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:81781980..81782760(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000001390
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000000157
• Aliases: None
• Description: None

Sequence

>retro_cjac_1229
GATGTCAAGACGCCATCCACCATCCAGATCTGCAGGGTCATGCGGCCAGATGATGCCAACATGGTCGGCAATGTCCATGG
GGAACCATCCTGAAGATGATTGAGGAGGCGGGTGCCATCATCAGCACCTGGCATTGCAACAGCCAGAACGGGGAGCACTG
TGTAGCTGTGCTGGCTTGGGTTGAGTGCACCAACTTCCTGTCGCCCATGTGCAGCCAGGAGGTGGCCCATGTCAGCGCGG
AGATCACCTATACCACCTATAAGCACTCGGTGGAGGTGCAGGTCAACGTGTTGTCTGAAAACATCCTCACAGGTGCCAAA
AAGTTGACCAATAAGGCCACCCTCTGGTATGTGCCCCTGTCGCTGAAGAATGTGGACAAGGTCCTCGAGGTGCCTCCTGT
TGTGTATTCCCGGCAGGAGCAGGAGGAGGAGGGCCGGAAGCCTTATGAAGCTCAGAAGCTGGAGCACGTGGAGACCAAGT
GGAGGAACGGGGACATCATCCAGCCAGCCCTCAACCCAGAGCCAAACACTATCAGCTACAGCCAGTCCAGCTTGATTCAC
CTGGTGTGGCCTTCAGACTGTACCCTACACGGCCTTGTGCATGGAGGTGTGACCATGAAGCTCATGGACGAGGTCGCCGG
GATCGTGGCTGCACGTCACTGCAAGACCAGCATCGTCACAGCTTCCAGGGACGCCACTAATTTTCACAACAAGATCAGAA
AAGGCTTCGGTCATCACCATCTCAGGACGAATGACCTTCACGAGCAATAAGTCCATGGAG

Alignment

ORF - retro_cjac_1229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.81 %
• Parental protein coverage: 68.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLPPSGAYTTARIMRPDDANVAGNVHG-GTILKMIEEAGAIISTRHCNSQNGERCVAALARVERTDFLSP
          D..........R.MRPDDAN..GNVHG.GTILKMIEEAGAIIST.HCNSQNGE.CVA.LA.VE.T.FLSP
Retrocopy DVKTPSTIQICRVMRPDDANMVGNVHG<GTILKMIEEAGAIISTWHCNSQNGEHCVAVLAWVECTNFLSP

Parental  MCIGEVAHVSAEITYTS-KHSVEVQVNVLSENILTGAKKLTNNATLWYVP-SLKNVDNKVLEVPPVVFCR
          MC..EVAHVSAEITYT..KHSVEVQVNVLSENILTGAKKLTN.ATLWYVP.SLKNVD.KVLEVPPVV..R
Retrocopy MCSQEVAHVSAEITYTTYKHSVEVQVNVLSENILTGAKKLTNKATLWYVPLSLKNVD-KVLEVPPVVYSR

Parental  HSQQRSGPASKPASCLSRFGTPWHEGDAGQGILLPEPNTVSYSQSSLIHLVGPSDCTLHGFVHGGVTMKL
          ..Q...G.....A..L....T.W..GD..Q..L.PEPNT.SYSQSSLIHLV.PSDCTLHG.VHGGVTMKL
Retrocopy QEQEEEGRKPYEAQKLEHVETKWRNGDIIQPALNPEPNTISYSQSSLIHLVWPSDCTLHGLVHGGVTMKL

Parental  MDEVAGIVAARHCKTNIVTASVDAINFHDKIRKGF-VITISGRMTFTSNKSME
          MDEVAGIVAARHCKT.IVTAS.DA.NFH.KIRKGF.VITISGRMTFTSNKSME
Retrocopy MDEVAGIVAARHCKTSIVTASRDATNFHNKIRKGF>VITISGRMTFTSNKSME

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	28.93 RPM
SRP051959_heart	0.00 RPM	6.26 RPM
SRP051959_kidney	0.00 RPM	14.84 RPM
SRP051959_liver	0.00 RPM	12.48 RPM
SRP051959_lung	0.00 RPM	4.93 RPM
SRP051959_lymph_node	0.00 RPM	5.37 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.65 RPM
SRP051959_spleen	0.00 RPM	6.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1229 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1229 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1229 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000157	2 retrocopies	retro_cjac_1229 , retro_cjac_457,
Homo sapiens	ENSG00000097021	1 retrocopy	retro_hsap_3034,
Mustela putorius furo	ENSMPUG00000006882	1 retrocopy	retro_mputfur_177,
Nomascus leucogenys	ENSNLEG00000010371	1 retrocopy	retro_nleu_845,
Pongo abelii	ENSPPYG00000001945	1 retrocopy	retro_pabe_2513,
Pan troglodytes	ENSPTRG00000000084	1 retrocopy	retro_ptro_2047,