RetrogeneDB ID: retro_cjac_675

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:40810522..40810846(+)
• Located in intron of: ENSCJAG00000021006

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC8
• Ensembl ID: ENSCJAG00000017312
• Aliases: None
• Description: ER membrane protein complex subunit 8 [Source:HGNC Symbol;Acc:7864]

Sequence

>retro_cjac_675
AGTCCAAACCAGGTTGCAGAGAAGGTATCTTCCGGAATCGCTGAGGGCTTCAGTGATACTGCACTCATCATGGTAGACAA
CACCAAGTTCACGATGTACTGCATAGTGCCTACAATCCACATGTACGAGCACCATGAGAACAGACGGCAGTGCAGAGACC
CACACCATGACTAGTGTGAAGACGGGCCAGAGGCGCAGAGGATCTCTGTATCACTCCTGGACAGCTGGTACTACCAGATG
CTTGTAGATCTCAATAACCAGCTGGATAACATTCAGAATGACTGGACAAACCCAGAGATCAATAAAGCTGTTCTGCACCT
GTGC

Alignment

ORF - retro_cjac_675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.48 %
• Parental protein coverage: 51.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPNQVAEKVASRIAEGFSDTALIMVDNTKFTMDCVAPTIHVYEHHENRWRCRDPHHDYCEDWPEAQRISA
          SPNQVAEKV.S.IAEGFSDTALIMVDNTKFTM.C..PTIH.YEHHENR..CRDPHHD.CED.PEAQRIS.
Retrocopy SPNQVAEKVSSGIAEGFSDTALIMVDNTKFTMYCIVPTIHMYEHHENRRQCRDPHHD*CEDGPEAQRISV

Parental  SLLDSRSYETLVDFDNHLDDIRNDWTNPEINKAVLHLC
          SLLDS..Y..LVD..N.LD.I.NDWTNPEINKAVLHLC
Retrocopy SLLDSWYYQMLVDLNNQLDNIQNDWTNPEINKAVLHLC

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	0.02 RPM	4.28 RPM
SRP051959_heart	0.02 RPM	4.81 RPM
SRP051959_kidney	0.04 RPM	4.86 RPM
SRP051959_liver	0.06 RPM	7.43 RPM
SRP051959_lung	0.03 RPM	5.37 RPM
SRP051959_lymph_node	0.02 RPM	5.96 RPM
SRP051959_skeletal_muscle	0.07 RPM	8.08 RPM
SRP051959_spleen	0.08 RPM	3.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_675 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_675 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019922	1 retrocopy	retro_cfam_2117,
Callithrix jacchus	ENSCJAG00000017312	1 retrocopy	retro_cjac_675 ,
Erinaceus europaeus	ENSEEUG00000011856	1 retrocopy	retro_eeur_44,
Macropus eugenii	ENSMEUG00000009360	5 retrocopies	retro_meug_1050, retro_meug_1386, retro_meug_636, retro_meug_709, retro_meug_97,
Monodelphis domestica	ENSMODG00000004596	1 retrocopy	retro_mdom_163,
Otolemur garnettii	ENSOGAG00000010372	1 retrocopy	retro_ogar_2503,