RetrogeneDB ID: retro_cjac_896

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:20901692..20902148(-)
• Located in intron of: ENSCJAG00000007685

Retrocopy information

• Ensembl ID: ENSCJAG00000007695
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FUNDC1
• Ensembl ID: ENSCJAG00000010876
• Aliases: None
• Description: FUN14 domain containing 1 [Source:HGNC Symbol;Acc:28746]

Sequence

>retro_cjac_896
GCAACCCAGAAACCCCCTCCTCAAGAATCTGAAAGTGATGACGCTTATGAAGCACAGGATTTAACTGAGTATGCAGGAAG
ACACCAGTGGTGGAATCTAGTGTTTGGCCACAGTTTGAGACCTATGGTAGAAAAAATGCTCGATAGCTACCCAGATTGAA
TGGATGGTGTTACTGGCCGGTGTGCAGGATTGTTGTTCCAAAAAGTTCGAAAACTCGCAGCAACTGCAGTAGGTGGTGGC
TTTGTTCTCCTTCAGATTGCTAGTCCTAGTGGCTACCTGCAGATTGGCTGGAAGAGAGTTGAAAAAGATTCAAACAAAGC
AAAAAGACACATTAAGAAACAGGTGAACGAAACAGCACCTGAATTCAACAATTTAATTGAAGAAGCAACAGAACGTATCA
AGCAATTTATTGTGATATTCAGTGGATTTGCGGGAGGCTTTTTGCTCGGACTTGCA

Alignment

ORF - retro_cjac_896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.42 %
• Parental protein coverage: 98.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ATRNPPPQEYESDDDSYEVLDLTEYARRHQWWNRVFGHSSGPMVEKY-SVATQIV-MGGVTGWCAGFLFQ
          AT..PPPQE.ESDD..YE..DLTEYA.RHQWWN.VFGHS..PMVEK..S.ATQI..M.GVTG.CAG.LFQ
Retrocopy ATQKPPPQESESDD-AYEAQDLTEYAGRHQWWNLVFGHSLRPMVEKM>SIATQIE<MDGVTGRCAGLLFQ

Parental  KVGKLAATAVGGGFLLLQIASHSGYVQIDWKRVEKDVNKAKRQIKKRANKAAPEINNLIEEATEFIKQNI
          KV.KLAATAVGGGF.LLQIAS.SGY.QI.WKRVEKD.NKAKR.IKK..N..APE.NNLIEEATE.IKQ.I
Retrocopy KVRKLAATAVGGGFVLLQIASPSGYLQIGWKRVEKDSNKAKRHIKKQVNETAPEFNNLIEEATERIKQFI

Parental  VISSGFVGGFLLGLA
          VI.SGF.GGFLLGLA
Retrocopy VIFSGFAGGFLLGLA

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	0.16 RPM	1.93 RPM
SRP051959_heart	0.07 RPM	3.47 RPM
SRP051959_kidney	0.16 RPM	3.95 RPM
SRP051959_liver	0.00 RPM	1.73 RPM
SRP051959_lung	0.26 RPM	3.04 RPM
SRP051959_lymph_node	0.02 RPM	3.22 RPM
SRP051959_skeletal_muscle	0.02 RPM	2.82 RPM
SRP051959_spleen	0.15 RPM	2.94 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_896 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_896 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_896 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004287	3 retrocopies	retro_cjac_1977, retro_cjac_2387, retro_cjac_651,
Callithrix jacchus	ENSCJAG00000010876	1 retrocopy	retro_cjac_896 ,
Cavia porcellus	ENSCPOG00000012962	2 retrocopies	retro_cpor_507, retro_cpor_508,
Echinops telfairi	ENSETEG00000012763	3 retrocopies	retro_etel_1614, retro_etel_697, retro_etel_852,
Homo sapiens	ENSG00000069509	1 retrocopy	retro_hsap_936,
Gorilla gorilla	ENSGGOG00000023311	1 retrocopy	retro_ggor_755,
Latimeria chalumnae	ENSLACG00000010215	1 retrocopy	retro_lcha_74,
Macropus eugenii	ENSMEUG00000006795	5 retrocopies	retro_meug_1597, retro_meug_2127, retro_meug_232, retro_meug_415, retro_meug_994,
Microcebus murinus	ENSMICG00000000450	2 retrocopies	retro_mmur_1189, retro_mmur_1461,
Macaca mulatta	ENSMMUG00000003505	1 retrocopy	retro_mmul_38,
Monodelphis domestica	ENSMODG00000021088	3 retrocopies	retro_mdom_1262, retro_mdom_769, retro_mdom_917,
Nomascus leucogenys	ENSNLEG00000002513	2 retrocopies	retro_nleu_2760, retro_nleu_294,
Oryctolagus cuniculus	ENSOCUG00000029753	5 retrocopies	retro_ocun_1008, retro_ocun_1376, retro_ocun_1567, retro_ocun_27, retro_ocun_314,
Pongo abelii	ENSPPYG00000020268	2 retrocopies	retro_pabe_806, retro_pabe_829,
Pelodiscus sinensis	ENSPSIG00000013793	1 retrocopy	retro_psin_30,
Pan troglodytes	ENSPTRG00000021821	1 retrocopy	retro_ptro_648,
Rattus norvegicus	ENSRNOG00000003470	1 retrocopy	retro_rnor_2644,
Sarcophilus harrisii	ENSSHAG00000000501	1 retrocopy	retro_shar_222,
Tarsius syrichta	ENSTSYG00000009139	1 retrocopy	retro_tsyr_1522,