RetrogeneDB ID: retro_cjac_2169

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:110764711..110765176(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C18orf21
• Ensembl ID: ENSCJAG00000021041
• Aliases: None
• Description: chromosome 18 open reading frame 21 [Source:HGNC Symbol;Acc:28802]

Sequence

>retro_cjac_2169
GATAAGAGCACTTTTGAAGAAACATATCTGTACTGTTTGCAGTTGTTGGTTCTGGATAACTCTCGAGTGTGTCTCAAATC
CAAAGCCACATTGGTACCCCAAATACAGAAACGGTTTAATTAAGGAGCATGAAATTATACACTCAGTTTTAAAGAAGCAA
AAATTGTGAAAAAGTTCAAAGGCTCCAAAAATGTTGTAATCAACAACTTGTAAAATATGCAACAGAACAGTGAAACATCA
TGGTAAGAGTAAAAGCTTTCTATCAGCATTGACTAGCAATCCTACCACTCCTACAAGTAAACTCAGCCTGAACACACCAA
AGAAAAGGACTGCAAACCCAAACCATGATATGTCTGGTTCTAAAGGCAAGAGACCGGTATCAATTTTGAGAACACCTACA
TCTGGATAGTCAGTATTTTCTTGCTTCTCAAACATGTGAGCAAAACAAAGAGACATTTTTCTCAA

Alignment

ORF - retro_cjac_2169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.43 %
• Parental protein coverage: 71.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DKSTFEETCPYCFQLLLLDNSRVRLKPKAKMTPKIQKLLNREARNYTLSFKEAKIVKKFKDSKSVLL-IT
          DKSTFEET..YC.QLL.LDNSRV.LK.KA...P.IQK..N..A.NYTLSFKEAKIVKKFK.SK.V....T
Retrocopy DKSTFEETYLYCLQLLVLDNSRVCLKSKATLVPQIQKRFN*GA*NYTLSFKEAKIVKKFKGSKNVVI>TT

Parental  CKTCNRTVKHHGKSRSFLATLKSSPTTPTSKLTLKTPERRTVDPNRDKSGSKGKSPALIFRTPTSGQSVS
          CK.CNRTVKHHGKS.SFL..L.S.PTTPTSKL.L.TP..RT..PN.D.SGSKGK.P..I.RTPTSG.SV.
Retrocopy CKICNRTVKHHGKSKSFLSALTSNPTTPTSKLSLNTPKKRTANPNHDMSGSKGKRPVSILRTPTSG*SVF

Parental  TSSS-KSMSKTKKHFSQ
          ...S.K..SKTK.HFSQ
Retrocopy SCFS<KHVSKTKRHFSQ

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	5.39 RPM
SRP051959_heart	0.00 RPM	5.56 RPM
SRP051959_kidney	0.00 RPM	7.85 RPM
SRP051959_liver	0.00 RPM	7.06 RPM
SRP051959_lung	0.00 RPM	8.51 RPM
SRP051959_lymph_node	0.00 RPM	11.23 RPM
SRP051959_skeletal_muscle	0.02 RPM	7.10 RPM
SRP051959_spleen	0.00 RPM	8.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2169 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2169 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2169 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3062
Pan troglodytes	retro_ptro_1981
Gorilla gorilla	retro_ggor_2102
Pongo abelii	retro_pabe_2536
Macaca mulatta	retro_mmul_1876

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029548	1 retrocopy	retro_cfam_1636,
Callithrix jacchus	ENSCJAG00000021041	2 retrocopies	retro_cjac_1030, retro_cjac_2169 ,
Cavia porcellus	ENSCPOG00000025449	1 retrocopy	retro_cpor_1461,
Felis catus	ENSFCAG00000000626	1 retrocopy	retro_fcat_1717,
Homo sapiens	ENSG00000141428	1 retrocopy	retro_hsap_3062,
Gorilla gorilla	ENSGGOG00000026334	1 retrocopy	retro_ggor_2102,
Macaca mulatta	ENSMMUG00000018782	1 retrocopy	retro_mmul_1876,
Monodelphis domestica	ENSMODG00000025605	1 retrocopy	retro_mdom_260,
Mus musculus	ENSMUSG00000024273	2 retrocopies	retro_mmus_1676, retro_mmus_610,
Nomascus leucogenys	ENSNLEG00000006237	1 retrocopy	retro_nleu_1655,
Oryctolagus cuniculus	ENSOCUG00000028046	2 retrocopies	retro_ocun_1910, retro_ocun_435,
Ochotona princeps	ENSOPRG00000011163	2 retrocopies	retro_opri_1222, retro_opri_283,
Pongo abelii	ENSPPYG00000009110	1 retrocopy	retro_pabe_2536,
Pan troglodytes	ENSPTRG00000009973	2 retrocopies	retro_ptro_1981, retro_ptro_2935,
Pteropus vampyrus	ENSPVAG00000009174	3 retrocopies	retro_pvam_1086, retro_pvam_1488, retro_pvam_629,
Tupaia belangeri	ENSTBEG00000016670	1 retrocopy	retro_tbel_4056,
Tarsius syrichta	ENSTSYG00000010817	2 retrocopies	retro_tsyr_1675, retro_tsyr_1787,