RetrogeneDB ID: retro_cjac_2314

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:22291298..22291529(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAPC5
• Ensembl ID: ENSCJAG00000007484
• Aliases: None
• Description: small nuclear RNA activating complex, polypeptide 5, 19kDa [Source:HGNC Symbol;Acc:15484]

Sequence

>retro_cjac_2314
CAGGAACTGCGCAAGGAGGAGGCGATGCTGCTGCTGTTGAATGCAGCCCTGTGTGACCAGCTGAACCGTGTCAAGGTTGA
AGCCTTGGCCCTTCAATCAATGAGTGATTCTAGAAGAGGGGATGAGATGCTGTCTTCTCCAACTGCGCCTGAACAGCCAT
ATGTCATGTACGTACATGTAGACAATAAAGCATCTGTCAACCCACCTACACTGGAGTGAAGCATAGAGTCC

Alignment

ORF - retro_cjac_2314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 78.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QELRKEEETLLRLKAALHDQLNRLKVEELALQSMISSRRGDEMLSSQTVPEQSHDMLVHVDNEASINQTT
          QELRKEE..LL.L.AAL.DQLNR.KVE.LALQSM..SRRGDEMLSS.T.PEQ...M.VHVDN.AS.N..T
Retrocopy QELRKEEAMLLLLNAALCDQLNRVKVEALALQSMSDSRRGDEMLSSPTAPEQPYVMYVHVDNKASVNPPT

Parental  LELSTKS
          LE.S..S
Retrocopy LE*SIES

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	2.40 RPM
SRP051959_heart	0.00 RPM	4.05 RPM
SRP051959_kidney	0.00 RPM	4.33 RPM
SRP051959_liver	0.00 RPM	1.84 RPM
SRP051959_lung	0.00 RPM	2.88 RPM
SRP051959_lymph_node	0.00 RPM	3.20 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.80 RPM
SRP051959_spleen	0.00 RPM	3.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2314 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2314 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2314 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017304	1 retrocopy	retro_cfam_1063,
Callithrix jacchus	ENSCJAG00000007484	1 retrocopy	retro_cjac_2314 ,
Dasypus novemcinctus	ENSDNOG00000006689	1 retrocopy	retro_dnov_1203,
Gorilla gorilla	ENSGGOG00000003693	1 retrocopy	retro_ggor_2398,
Macropus eugenii	ENSMEUG00000003990	1 retrocopy	retro_meug_1590,
Macaca mulatta	ENSMMUG00000016841	1 retrocopy	retro_mmul_1815,
Mus musculus	ENSMUSG00000032398	1 retrocopy	retro_mmus_702,
Nomascus leucogenys	ENSNLEG00000012935	1 retrocopy	retro_nleu_2325,
Oryctolagus cuniculus	ENSOCUG00000008791	1 retrocopy	retro_ocun_1059,
Rattus norvegicus	ENSRNOG00000010156	1 retrocopy	retro_rnor_1087,
Ictidomys tridecemlineatus	ENSSTOG00000009201	1 retrocopy	retro_itri_1582,
Tupaia belangeri	ENSTBEG00000014333	1 retrocopy	retro_tbel_68,