RetrogeneDB ID: retro_cjac_940

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:114630563..114631274(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000008394
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ETHE1
• Ensembl ID: ENSCJAG00000013606
• Aliases: None
• Description: ethylmalonic encephalopathy 1 [Source:HGNC Symbol;Acc:23287]

Sequence

>retro_cjac_940
GGTCAGCCAGCGGCAGCTGAGCCAGCGCGGCAGATGTTCTAGCCGGTGAGTTGCACCTACACGTACCTGCTGGGTGACAG
AGAGTCCCGGGATGCCATTCTGATCGACCCGGTCCTGGAGACAGCGCCTCGGGATGCCCAGCTGATCAAGGAACTGGGGC
TGCGGCTGCTGTATGCTGTGAATACCCACTGCCACGCGGACCACATTACAGGCTCTGGGCTACTCCATTCCCTCCTCCCT
GGCTGCCAGTCTGTCATCTCCCGCCTTAGTGGGGCCCAGGCTGACTTGCACATTGAGGATGGAGACTCCATCTGCTTCGG
GAGCTTCGCCTTGGAGACCAGGGCCAGTCCTGGCCACACCCCAGGCTGTGTCACCTTCGTCCTGAATGACCAAAGCATGG
CCTTCACTGGAGATGCCCTGTTGATCCGTGGGTGTGGACGGACAGACTTCCAGCAAGGCTGTGCCGAGACCTTGTACCAC
TCGGTCCATGAAAAGATCTTCACACTTCCAGGCAACTGTCTGGTCTACCCTGCTCATGATTACCATGGGTTCACAGTGTC
CACCGTGGAGGAGAGGACTCTGAACCCTCGGCTCACCTTCAGCTGTGAGGAGTTTGTCAAACTCATGGACAACCTGAACT
TGCCTAAACCTCAACAGATAGACTTTGCTGTTCCTGCCAACATGCGCTGTGGGGTGCAGACATCCACTTCC

Alignment

ORF - retro_cjac_940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.86 %
• Parental protein coverage: 93.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRSEAPILLRQMFEPVSCTYTYLLGDRESREAVLIDPVLETAPRDAQLIKELGLRLLYAVNTHCHADHIT
          G...A....RQMF.PVSCTYTYLLGDRESR.A.LIDPVLETAPRDAQLIKELGLRLLYAVNTHCHADHIT
Retrocopy GQPAAAEPARQMF*PVSCTYTYLLGDRESRDAILIDPVLETAPRDAQLIKELGLRLLYAVNTHCHADHIT

Parental  GSGLLRSLLPGCQSVISSLSGAQADLHIEDGDSIRFGRFALETRASPGHTPGCVTFVLNDQSMAFTGDAL
          GSGLL.SLLPGCQSVIS.LSGAQADLHIEDGDSI.FG.FALETRASPGHTPGCVTFVLNDQSMAFTGDAL
Retrocopy GSGLLHSLLPGCQSVISRLSGAQADLHIEDGDSICFGSFALETRASPGHTPGCVTFVLNDQSMAFTGDAL

Parental  LIRGCGRTDFQQGCAKTLYHSVHEKIFTLPGNCLVYPAHDYHGFTVSTVEEERTLNPRLTLSCEEFVKLM
          LIRGCGRTDFQQGCA.TLYHSVHEKIFTLPGNCLVYPAHDYHGFTVSTV.EERTLNPRLT.SCEEFVKLM
Retrocopy LIRGCGRTDFQQGCAETLYHSVHEKIFTLPGNCLVYPAHDYHGFTVSTV-EERTLNPRLTFSCEEFVKLM

Parental  DNLNLPKPQQIDFAVPANMRCGVQTSTS
          DNLNLPKPQQIDFAVPANMRCGVQTSTS
Retrocopy DNLNLPKPQQIDFAVPANMRCGVQTSTS

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	0.27 RPM	23.72 RPM
SRP051959_heart	0.18 RPM	3.37 RPM
SRP051959_kidney	0.13 RPM	5.86 RPM
SRP051959_liver	0.45 RPM	4.48 RPM
SRP051959_lung	0.16 RPM	6.56 RPM
SRP051959_lymph_node	0.53 RPM	8.26 RPM
SRP051959_skeletal_muscle	0.07 RPM	3.89 RPM
SRP051959_spleen	0.59 RPM	7.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_940 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_940 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013606	1 retrocopy	retro_cjac_940 ,