RetrogeneDB ID: retro_cjac_1352

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:72194872..72195203(+)
• Located in intron of: ENSCJAG00000006554

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_1352
ATAGAGACTGAGACCAGTGGCCCAGAGCGACCTCCCGAGAAGCCACGGAAACATGACAGTGGTGCGGTAGACTTGGAGCT
CGTCACCGACTATGCAGAGGAGAAGGGAATCCAGAGTTCCAACCTGGAGATGGCCATGTCTGTGATCGGAGACAGAAAGT
CCCGGGAGCAAAAAGCCAAACAGGAGCATGAGAAAGAACTGGCAAAGGCACTGTCAGGAAGGAAGATCTGGAGCTGATAA
GGACCGAGATGGAGCTATCTCAAGCAGCAACAGAAGGCAGCTTGGGGAACACATGGGCAATGTGTTAGAGGTGCTTATTG
CCCCAACCAAC

Alignment

ORF - retro_cjac_1352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.42 %
• Parental protein coverage: 63.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LETETSGPERPPEKPRKHDSGAADLERVTDYAEEKEIQSSNLETAMSVIGDRRSREQKAKQEREKELAKV
          .ETETSGPERPPEKPRKHDSGA.DLE.VTDYAEEK.IQSSNLE.AMSVIGDR.SREQKAKQE.EKELAK.
Retrocopy IETETSGPERPPEKPRKHDSGAVDLELVTDYAEEKGIQSSNLEMAMSVIGDRKSREQKAKQEHEKELAKA

Parental  -TIKKEDLELIMTEMEISRAAAE-RSLREHMGNVVEALIALTN
          .T..KEDLELI.TEME.S.AA.E.R.L.EHMGNV.E.LIA.TN
Retrocopy <TVRKEDLELIRTEMELSQAATE<RQLGEHMGNVLEVLIAPTN

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	0.20 RPM	21.34 RPM
SRP051959_heart	0.12 RPM	20.21 RPM
SRP051959_kidney	0.22 RPM	20.72 RPM
SRP051959_liver	0.11 RPM	22.77 RPM
SRP051959_lung	0.23 RPM	20.53 RPM
SRP051959_lymph_node	0.30 RPM	17.69 RPM
SRP051959_skeletal_muscle	0.15 RPM	24.33 RPM
SRP051959_spleen	0.19 RPM	22.33 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1352 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1352 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1352 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,