RetrogeneDB ID: retro_cjac_3098

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:121030600..121030936(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11orf58
• Ensembl ID: ENSCJAG00000009626
• Aliases: None
• Description: chromosome 11 open reading frame 58 [Source:HGNC Symbol;Acc:16990]

Sequence

>retro_cjac_3098
AGGGAGTCCTACCCTTACAGGGTGAAGTGTTAAGTTTTCACAGACAACAATCTTGGATCTAGCAATTGGCAATTAGCAAA
CTTAGGTAATGAAGAAAGAAAGCATCTTAAGACATGGGTGTAGAAAAGAAAGAACATACTGACAGTCTTGTTGCAAGAGA
TCAAAAATCAACATCTTACTTCTGAAAAGGGGAAAGAAGACAAGAAAACTAAGGAAGAACTGGAGTTTCAACATCAGCCA
GGTGTCAATAGTCAGTTTTCAGGAAGATACAGATGACATTGTGAATTTGGCTTCAGTGAAGTACATCATGATGAAGAAGG
CAATACAGCTGGAGAG

Alignment

ORF - retro_cjac_3098 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.41 %
• Parental protein coverage: 62.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RESHPHGVKRSASPDDDLGSSNWEAADLGNEERKQKFLRL-MGAGKKEHTGRLVIGDHKSTSHF-RTGEE
          RES.P..VK.....D..LGSSNW..A.LGNEE...K.L...MG..KKEHT..LV..D.KSTS.F...G.E
Retrocopy RESYPYRVKC*VFTDNNLGSSNWQLANLGNEE--RKHLKT<MGVEKKEHTDSLVARDQKSTSYF>EKGKE

Parental  DKKINEELESQYQQSMDSKLSGRYRRHCGLGFSEVEDHDGEGDVAGD
          DKK..EELE.Q.Q....S..SGRYR.HC..GFSEV..HD.EG..AG.
Retrocopy DKKTKEELEFQHQPGVNSQFSGRYR*HCEFGFSEVH-HDEEGNTAGE

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	33.81 RPM
SRP051959_heart	0.00 RPM	44.48 RPM
SRP051959_kidney	0.02 RPM	46.46 RPM
SRP051959_liver	0.00 RPM	42.43 RPM
SRP051959_lung	0.00 RPM	47.39 RPM
SRP051959_lymph_node	0.00 RPM	38.65 RPM
SRP051959_skeletal_muscle	0.02 RPM	37.39 RPM
SRP051959_spleen	0.04 RPM	46.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3098 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3098 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3098 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3898

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030220	2 retrocopies	retro_cfam_160, retro_cfam_717,
Callithrix jacchus	ENSCJAG00000009626	1 retrocopy	retro_cjac_3098 ,
Cavia porcellus	ENSCPOG00000009679	2 retrocopies	retro_cpor_1331, retro_cpor_772,
Equus caballus	ENSECAG00000011778	1 retrocopy	retro_ecab_269,
Felis catus	ENSFCAG00000027747	1 retrocopy	retro_fcat_2016,
Homo sapiens	ENSG00000110696	2 retrocopies	retro_hsap_1408, retro_hsap_3898,
Macropus eugenii	ENSMEUG00000011795	1 retrocopy	retro_meug_1432,
Myotis lucifugus	ENSMLUG00000001589	1 retrocopy	retro_mluc_2604,
Monodelphis domestica	ENSMODG00000007147	2 retrocopies	retro_mdom_1249, retro_mdom_672,
Mus musculus	ENSMUSG00000030663	2 retrocopies	retro_mmus_2190, retro_mmus_2616,
Nomascus leucogenys	ENSNLEG00000017719	1 retrocopy	retro_nleu_1425,
Otolemur garnettii	ENSOGAG00000025335	2 retrocopies	retro_ogar_1613, retro_ogar_2569,
Ochotona princeps	ENSOPRG00000000154	1 retrocopy	retro_opri_761,
Pongo abelii	ENSPPYG00000003458	2 retrocopies	retro_pabe_1166, retro_pabe_3178,
Rattus norvegicus	ENSRNOG00000020436	1 retrocopy	retro_rnor_622,