RetrogeneDB ID: retro_cjac_1913

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:62247502..62247818(-)
• Located in intron of: ENSCJAG00000007106

Retrocopy information

• Ensembl ID: ENSCJAG00000031858
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FIS1
• Ensembl ID: ENSCJAG00000016053
• Aliases: None
• Description: fission 1 (mitochondrial outer membrane) homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21689]

Sequence

>retro_cjac_1913
CTGATGCTGACCAACTATAATGACGACATCTGTAAAGGCATCAAGCTGCTTGAGGAGCTGCTGCCCAAAGGGAACAAAGA
AGAGAAGCAGGATTATGTCTTCTACCTGACTGTGGGGAACTACCAACTCAAGAAATATGAAAAGGCCCTAAAGTATATTC
AAGAACTGCTACAGACAGAGCCCCAGAACACCAAGGCCAAGGAACTAGAACCGTTTCACAGGCAAGGTCATGAAGAAAGA
TAAACTAGTGGGCATGGCCATCATTAGAGGCATGGCCATCATTGGAGGCATGGCCCTGGGCGTGGCAGGACTGGCT

Alignment

ORF - retro_cjac_1913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.43 %
• Parental protein coverage: 69.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVRSKYNDDILKGVALLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQTEPENNQAKELE
          L....YNDDI.KG..LLEELLPKG.KEE..DYVFYL.VGNY.LK.YEKALKY...LLQTEP.N..AKELE
Retrocopy LMLTNYNDDICKGIKLLEELLPKGNKEEKQDYVFYLTVGNYQLKKYEKALKYIQELLQTEPQNTKAKELE

Parental  -RLIDKAMKKDGLVGMAIVGGMALGVAGLAGLIGLA
          .R...K.MKKD.LV................G..GLA
Retrocopy >RFTGKVMKKDKLVXXXXXXXXXXXXXXXLGVAGLA

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	8.59 RPM
SRP051959_heart	0.18 RPM	18.72 RPM
SRP051959_kidney	0.22 RPM	22.16 RPM
SRP051959_liver	0.06 RPM	21.96 RPM
SRP051959_lung	0.37 RPM	15.86 RPM
SRP051959_lymph_node	0.32 RPM	7.76 RPM
SRP051959_skeletal_muscle	0.04 RPM	43.83 RPM
SRP051959_spleen	0.23 RPM	11.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1913 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1913 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1913 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013800	2 retrocopies	retro_cfam_557, retro_cfam_755,
Callithrix jacchus	ENSCJAG00000016053	1 retrocopy	retro_cjac_1913 ,
Loxodonta africana	ENSLAFG00000020494	1 retrocopy	retro_lafr_702,
Myotis lucifugus	ENSMLUG00000024207	1 retrocopy	retro_mluc_168,
Monodelphis domestica	ENSMODG00000005034	1 retrocopy	retro_mdom_1773,
Otolemur garnettii	ENSOGAG00000028158	1 retrocopy	retro_ogar_1544,
Rattus norvegicus	ENSRNOG00000001420	2 retrocopies	retro_rnor_1659, retro_rnor_1689,
Sus scrofa	ENSSSCG00000027757	1 retrocopy	retro_sscr_1083,