RetrogeneDB ID: retro_cjac_3951

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286400.1:917588..918119(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPZ1
• Ensembl ID: ENSCJAG00000018887
• Aliases: None
• Description: coatomer protein complex, subunit zeta 1 [Source:HGNC Symbol;Acc:2243]

Sequence

>retro_cjac_3951
ATGGAGGCGCTGATTTTGGAACCTTCCCTGTATACTGCCAAAGCCATCCTGATTCTGGACAATGATGGAGATCGACTTTT
TGCGAAGTACTATGACGACACCTACCCCAGTGTCAAGGAGCAAAAGACCTTTGAGAAGAACATCTTCAACAAGACCCATC
AGACTGACAGTGAAATTGCACTCTTGGAAGGCCTGACAGTGGTATACAAAAGCAGTATAGATCTCTATTTCTATGTGATT
GGCAGCTCCTATGAAAATGAGCTGATGCTTATGGCTGTTCTAAACTGCCTCTTTGACTCATTGAGCCAGATGCGGAGGAA
AAATGTAGAAAAGTGAGCACTACTGGAGAACATGGAGGGGCTGTTCTTGGCTATGGATGAAATTGTAGATGGAGGGGTGA
TCCTAGAGAGTGATCCCCAGCAGGTGGTACACCGGGTGGCATTAAGGGGTGAAGATGTCCCCCTTACGGAGCAGACCATG
TCTCAGGTGCTGCAGTCAGCCAAAGAACAGATCAAGTGGTTGCTCCTTCGG

Alignment

ORF - retro_cjac_3951 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEALILEPSLYTVKAILILDNDGDRLFAKYYDDTYPSVKEQKAFEKNIFNKTHRTDSEIALLEGLTVVYK
          MEALILEPSLYT.KAILILDNDGDRLFAKYYDDTYPSVKEQK.FEKNIFNKTH.TDSEIALLEGLTVVYK
Retrocopy MEALILEPSLYTAKAILILDNDGDRLFAKYYDDTYPSVKEQKTFEKNIFNKTHQTDSEIALLEGLTVVYK

Parental  SSIDLYFYVIGSSYENELMLMAVLNCLFDSLSQMLRKNVEKRALLENMEGLFLAVDEIVDGGVILESDPQ
          SSIDLYFYVIGSSYENELMLMAVLNCLFDSLSQM.RKNVEK.ALLENMEGLFLA.DEIVDGGVILESDPQ
Retrocopy SSIDLYFYVIGSSYENELMLMAVLNCLFDSLSQMRRKNVEK*ALLENMEGLFLAMDEIVDGGVILESDPQ

Parental  QVVHRVALRGEDVPLTEQTVSQVLQSAKEQIKWSLLR
          QVVHRVALRGEDVPLTEQT.SQVLQSAKEQIKW.LLR
Retrocopy QVVHRVALRGEDVPLTEQTMSQVLQSAKEQIKWLLLR

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	22.54 RPM
SRP051959_heart	0.14 RPM	17.42 RPM
SRP051959_kidney	0.16 RPM	28.60 RPM
SRP051959_liver	0.41 RPM	25.95 RPM
SRP051959_lung	0.20 RPM	20.63 RPM
SRP051959_lymph_node	0.11 RPM	24.45 RPM
SRP051959_skeletal_muscle	6.94 RPM	18.72 RPM
SRP051959_spleen	0.19 RPM	20.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3951 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3951 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3951 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
Bos taurus	ENSBTAG00000005384	1 retrocopy	retro_btau_1500,
Canis familiaris	ENSCAFG00000006536	1 retrocopy	retro_cfam_30,
Callithrix jacchus	ENSCJAG00000018887	2 retrocopies	retro_cjac_1771, retro_cjac_3951 ,
Echinops telfairi	ENSETEG00000013499	1 retrocopy	retro_etel_1782,
Microcebus murinus	ENSMICG00000008401	1 retrocopy	retro_mmur_757,
Mus musculus	ENSMUSG00000060992	1 retrocopy	retro_mmus_2439,
Oryctolagus cuniculus	ENSOCUG00000013364	2 retrocopies	retro_ocun_1511, retro_ocun_797,
Rattus norvegicus	ENSRNOG00000036835	1 retrocopy	retro_rnor_2209,
Tupaia belangeri	ENSTBEG00000008730	1 retrocopy	retro_tbel_3749,
Tursiops truncatus	ENSTTRG00000001654	2 retrocopies	retro_ttru_114, retro_ttru_856,