RetrogeneDB ID: retro_cjac_1406

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:65878500..65878818(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATPIF1
• Ensembl ID: ENSCJAG00000009581
• Aliases: None
• Description: ATPase inhibitory factor 1 [Source:HGNC Symbol;Acc:871]

Sequence

>retro_cjac_1406
ATGGCAGTTACGGCGTTGGCGGCAAGGACGTGGCTTGGCGTTTGGGGCGTGAAGACCATGCGAGCCCGAAGCTTCGGCTC
GGATCAGTCTGAGAATCTCCATCGGGGCACGGGCTCCATCCGGGAAGCCGGTGGGGCCTTTGGAAAGAGAGAGAAGGCTG
AAGAGGAATGATATTTCTGAGCACAGACTAGAGAACAACTGGCAGCTTTGAAAAAACACCATGAAGATGAGCTCATTCAT
CATAAGAAGGAGATTGAGCATCTGCAGAAAGAAACTGAGCAGCATAAGCAGAAGATCAAAATACTAAAACATGATGAT

Alignment

ORF - retro_cjac_1406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVTALAARTWLGVWGVRTMQARSFGSDQSENLDRGAGSIREAGGAFGKREQAEEERYFRAQAREQLAAL
          MAVTALAARTWLGVWGV.TM.ARSFGSDQSENL.RG.GSIREAGGAFGKRE.AEEE.YF.AQ.REQLAAL
Retrocopy MAVTALAARTWLGVWGVKTMRARSFGSDQSENLHRGTGSIREAGGAFGKREKAEEE*YF*AQTREQLAAL

Parental  KKHHEDEIVHHKKEIERLQKEIERHKQKIKILKDDD
          KKHHEDE..HHKKEIE.LQKE.E.HKQKIKILK.DD
Retrocopy KKHHEDELIHHKKEIEHLQKETEQHKQKIKILKHDD

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	9.45 RPM
SRP051959_heart	0.00 RPM	25.29 RPM
SRP051959_kidney	0.00 RPM	24.01 RPM
SRP051959_liver	0.00 RPM	14.82 RPM
SRP051959_lung	0.00 RPM	14.28 RPM
SRP051959_lymph_node	0.00 RPM	9.06 RPM
SRP051959_skeletal_muscle	0.00 RPM	35.68 RPM
SRP051959_spleen	0.00 RPM	13.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1406 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1406 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032458	2 retrocopies	retro_cfam_1777, retro_cfam_651,
Callithrix jacchus	ENSCJAG00000009581	1 retrocopy	retro_cjac_1406 ,
Dasypus novemcinctus	ENSDNOG00000015460	1 retrocopy	retro_dnov_2592,
Myotis lucifugus	ENSMLUG00000000170	1 retrocopy	retro_mluc_363,
Mustela putorius furo	ENSMPUG00000015536	1 retrocopy	retro_mputfur_1570,
Mus musculus	ENSMUSG00000054428	2 retrocopies	retro_mmus_2516, retro_mmus_908,
Otolemur garnettii	ENSOGAG00000010337	2 retrocopies	retro_ogar_116, retro_ogar_268,
Rattus norvegicus	ENSRNOG00000013300	1 retrocopy	retro_rnor_2655,
Sorex araneus	ENSSARG00000010860	1 retrocopy	retro_sara_458,
Ictidomys tridecemlineatus	ENSSTOG00000020766	1 retrocopy	retro_itri_1240,