RetrogeneDB ID: retro_cjac_3011

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:106371050..106371491(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CASP3
• Ensembl ID: ENSCJAG00000005740
• Aliases: None
• Description: caspase 3, apoptosis-related cysteine peptidase [Source:HGNC Symbol;Acc:1504]

Sequence

>retro_cjac_3011
GGAACAAATGGACCTATTCACTAGAAAAAAATAAGTTTTCTCAGAGTGAACTGTTGCAGAAATCTAACTGGAAAACCCAA
GCTTTTCATTATTCAGCCCTGCCACAGTACAGAACTGGACCCTGGCATTGAAACAGACAGTGGTATTGATGATGACACGA
AGTGTCACAAAATACCAGTGGAAGCTGACTTCTTGTGTGCATATTCCATGGGACCTGGTTATTATTCTTGAAGAAATTCA
AAGGATGGCTCCTGGTTCATCCAGTCACTTTATGCCATGCTAAAACTATACACTGACAAGCTTGAGTTTATGCACATTCT
TACCAGGTTTAACTGAAAGGTGGGAAGAGAATTTGAGTCCTTTTCCCTTGATGCTACTTTCCATGCAAAGAAACAGATTC
CGTGTGTTGTGTTCATGCTCACAAAAGAACTGTATTTTTAT

Alignment

ORF - retro_cjac_3011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.05 %
• Parental protein coverage: 53.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTNGPVDLKKITSFFRGDCCRSLTGKPKLFIIQACRGTELDCGIETDSGVDDDMACHKIPVEADFLYAYS
          GTNGP...KKI.SF.R..CCR.LTGKPKLFIIQ.C..TELD.GIETDSG.DDD..CHKIPVEADFL.AYS
Retrocopy GTNGPIH*KKI-SFLRVNCCRNLTGKPKLFIIQPCHSTELDPGIETDSGIDDDTKCHKIPVEADFLCAYS

Parental  TAPGYYSWRNSRDGSWFIQSLCAMLKLYANKLEFMHILTRVNRKVATEFESSSFDATFHAKKQIPCIVSM
          ..PGYYS.RNS.DGSWFIQSL.AMLKLY..KLEFMHILTR.N.KV..EFES.S.DATFHAKKQIPC.V.M
Retrocopy MGPGYYS*RNSKDGSWFIQSLYAMLKLYTDKLEFMHILTRFN*KVGREFESFSLDATFHAKKQIPCVVFM

Parental  LTKELYFY
          LTKELYFY
Retrocopy LTKELYFY

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	14.20 RPM
SRP051959_heart	0.02 RPM	9.45 RPM
SRP051959_kidney	0.00 RPM	10.69 RPM
SRP051959_liver	0.00 RPM	10.09 RPM
SRP051959_lung	0.00 RPM	25.91 RPM
SRP051959_lymph_node	0.00 RPM	48.99 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.67 RPM
SRP051959_spleen	0.00 RPM	19.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3011 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3011 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3011 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005740	2 retrocopies	retro_cjac_2678, retro_cjac_3011 ,
Dasypus novemcinctus	ENSDNOG00000013931	1 retrocopy	retro_dnov_1013,
Dipodomys ordii	ENSDORG00000002554	2 retrocopies	retro_dord_178, retro_dord_620,
Homo sapiens	ENSG00000164305	1 retrocopy	retro_hsap_406,
Gorilla gorilla	ENSGGOG00000025155	1 retrocopy	retro_ggor_402,
Macaca mulatta	ENSMMUG00000012053	1 retrocopy	retro_mmul_114,
Nomascus leucogenys	ENSNLEG00000010895	1 retrocopy	retro_nleu_1005,
Pongo abelii	ENSPPYG00000015236	1 retrocopy	retro_pabe_312,
Pan troglodytes	ENSPTRG00000016640	1 retrocopy	retro_ptro_310,
Rattus norvegicus	ENSRNOG00000010475	1 retrocopy	retro_rnor_2747,
Sarcophilus harrisii	ENSSHAG00000009178	1 retrocopy	retro_shar_404,
Ictidomys tridecemlineatus	ENSSTOG00000003865	2 retrocopies	retro_itri_172, retro_itri_586,