RetrogeneDB ID: retro_cjac_2777

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:147982291..147982507(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2I
• Ensembl ID: ENSCJAG00000009671
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide I, 14.5kDa [Source:HGNC Symbol;Acc:9196]

Sequence

>retro_cjac_2777
TATGTCAACAAGATCACGCAAGAAGTGGATGAACTCACCCAGATTATTGCCGACATGTCCCAGGACCCCACGTTGCCACA
GACCGAGGACCACCCATGCCAGAAGTGCAGCCACAAGGGGACTGTGTTCTTCCAGTCACACAGAGCCTGGGTCAAAGATG
TCATGTGTCTGTACTACGTGTGCACGGCCCCACACTGCAGCCACCGCTGGACCGAG

Alignment

ORF - retro_cjac_2777 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.94 %
• Parental protein coverage: 57.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YVNKITHEVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCGHRW
          YVNKIT.EVDELTQIIAD.SQDPTLP.TEDHPCQKC.HK..VFFQSH.A...D.M.LYYVCTAPHC.HRW
Retrocopy YVNKITQEVDELTQIIADMSQDPTLPQTEDHPCQKCSHKGTVFFQSHRAWVKDVMCLYYVCTAPHCSHRW

Parental  TE
          TE
Retrocopy TE

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	3.15 RPM
SRP051959_heart	0.00 RPM	5.54 RPM
SRP051959_kidney	0.00 RPM	6.28 RPM
SRP051959_liver	0.00 RPM	3.68 RPM
SRP051959_lung	0.00 RPM	4.60 RPM
SRP051959_lymph_node	0.00 RPM	3.33 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.49 RPM
SRP051959_spleen	0.00 RPM	2.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2777 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2777 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2777 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006601	1 retrocopy	retro_cfam_1400,
Callithrix jacchus	ENSCJAG00000009671	1 retrocopy	retro_cjac_2777 ,
Dipodomys ordii	ENSDORG00000001852	2 retrocopies	retro_dord_264, retro_dord_555,
Monodelphis domestica	ENSMODG00000014172	1 retrocopy	retro_mdom_1465,
Mus musculus	ENSMUSG00000019738	1 retrocopy	retro_mmus_2287,
Oryctolagus cuniculus	ENSOCUG00000013044	2 retrocopies	retro_ocun_103, retro_ocun_1603,
Otolemur garnettii	ENSOGAG00000024254	1 retrocopy	retro_ogar_386,
Ochotona princeps	ENSOPRG00000001789	2 retrocopies	retro_opri_350, retro_opri_837,
Tursiops truncatus	ENSTTRG00000003919	1 retrocopy	retro_ttru_223,