RetrogeneDB ID: retro_cjac_748

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:130700288..130700561(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SERF2
• Ensembl ID: ENSCJAG00000002541
• Aliases: C10H15orf63, HYPK
• Description: None

Sequence

>retro_cjac_748
CGTGGTGAAATAGATATGGCGACCGAGGGGGACGTGGAGCTGGAGTTAGAGACGGAGACCAGTGGCCCATAGTGACCTCC
CGAGAAGCCACGGAAACATGACAGCGGCGCGGCGGACTTGGGGCGGGTCACCGACTACCCAGAGGGGAAGGAGATCCAGA
GTCCCAATGTGGAGACGGCCATGTCTGTGATTGGAGACAGAAGGCCCCGGGAGCAGAAAGCCAAACAGGAGCGGGACAAA
GAACTGGCAAAAGTCACTATCAAGAAGGGAGAT

Alignment

ORF - retro_cjac_748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.01 %
• Parental protein coverage: 52.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGEIDMATEGDVELELETETSGPERPPEKPRKHDSGAADLERVTDYAEEKEIQSSNLETAMSVIGDRRSR
          RGEIDMATEGDVELELETETSGP..PPEKPRKHDSGAADL.RVTDY.E.KEIQS.N.ETAMSVIGDRR.R
Retrocopy RGEIDMATEGDVELELETETSGP**PPEKPRKHDSGAADLGRVTDYPEGKEIQSPNVETAMSVIGDRRPR

Parental  EQKAKQEREKELAKVTIKKED
          EQKAKQER.KELAKVTIKK.D
Retrocopy EQKAKQERDKELAKVTIKKGD

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	21.34 RPM
SRP051959_heart	0.00 RPM	20.21 RPM
SRP051959_kidney	0.00 RPM	20.72 RPM
SRP051959_liver	0.02 RPM	22.77 RPM
SRP051959_lung	0.00 RPM	20.53 RPM
SRP051959_lymph_node	0.05 RPM	17.69 RPM
SRP051959_skeletal_muscle	0.00 RPM	24.33 RPM
SRP051959_spleen	0.02 RPM	22.33 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_748 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_748 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_748 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002541	2 retrocopies	retro_cjac_1352, retro_cjac_748 ,
Echinops telfairi	ENSETEG00000007464	3 retrocopies	retro_etel_1504, retro_etel_1616, retro_etel_1830,
Gorilla gorilla	ENSGGOG00000014809	1 retrocopy	retro_ggor_2557,
Macropus eugenii	ENSMEUG00000013059	1 retrocopy	retro_meug_1583,
Monodelphis domestica	ENSMODG00000017744	2 retrocopies	retro_mdom_26, retro_mdom_306,
Nomascus leucogenys	ENSNLEG00000005454	1 retrocopy	retro_nleu_2150,
Oryctolagus cuniculus	ENSOCUG00000001161	2 retrocopies	retro_ocun_1395, retro_ocun_967,
Otolemur garnettii	ENSOGAG00000010201	1 retrocopy	retro_ogar_1064,
Pongo abelii	ENSPPYG00000006424	1 retrocopy	retro_pabe_3108,
Pan troglodytes	ENSPTRG00000038721	1 retrocopy	retro_ptro_2582,
Rattus norvegicus	ENSRNOG00000015703	1 retrocopy	retro_rnor_2477,
Ictidomys tridecemlineatus	ENSSTOG00000006916	2 retrocopies	retro_itri_1861, retro_itri_1864,
Tursiops truncatus	ENSTTRG00000003726	1 retrocopy	retro_ttru_1499,