RetrogeneDB ID: retro_cjac_1929

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:78683409..78684059(-)
• Located in intron of: ENSCJAG00000019171

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPCS2
• Ensembl ID: ENSCJAG00000015576
• Aliases: None
• Description: signal peptidase complex subunit 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28962]

Sequence

>retro_cjac_1929
ATGGCGGCGGCAGCTGCACAGGCTGGAGAAGCGGTGGTAGCGGAGGCAGTACTGGGGCTGGTGGTGGTTCCAGCTGCGGG
GCAGGCATTGGCCGTAGTGGCTTGTTGGATAAGTGGCAGATAGACGATAAGTCTGTAAAAACTGACAAGTGGGATGGATC
AGCCGTGAAAAACTCTTTGGATGACTCTGCCAAAAAGGTACTTCTGGAAAAATACAAATATGTGGAGAATTTTGGTCTAA
TTGACGGTCGCCTCACCATCTGTACACTCTCTTGTTTCTTTGCCATAGTGGCTTTGATTTGGGATTATATGCACCCCTTT
GCAGAGTCCAAACCCGTTTTGGCTTTGTGCGTCATATCCTATTTTGTGATGATGGGGATTCTGACCATTTATACCTCATA
TAAGGAGAAGAGCATCTTCCTTGTGGCCCACAGGAAAGATCCTACAGGAATGGATCCTGATGATATTTGGCAGCTGTCCT
CCAGTCTTCAAAGGTTTAATGACAAATAAACCTTGAAGCTGACCTTCAGCAGTGGGAGAACAAAGCAGCAGCGGGAAGCC
GAGTTCACCAAGTCCGTTGCTAAGTTTTTTGACCACAGTGGGACACTGGTCATGGATGCATATGAGCCTGAAATATCCAG
GCTCCATGAC

Alignment

ORF - retro_cjac_1929 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.58 %
• Parental protein coverage: 96.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAAAQGG-RSGGSGGSSGAGGGSSCGTGIGRSGLLDKWKIDDKPVKIDKWDGSAVKNSLDDSAKKVLL
          MAAAAAQ.G.RSGGSGGS.GAGGGSSCG.GIGRSGLLDKW.IDDK.VK.DKWDGSAVKNSLDDSAKKVLL
Retrocopy MAAAAAQAG<RSGGSGGSTGAGGGSSCGAGIGRSGLLDKWQIDDKSVKTDKWDGSAVKNSLDDSAKKVLL

Parental  EKYKYVENFGLIDGRLTICTISCFFAIVALIWDYMHPFPESKPVLALCVISYFVMMGILTIYTSYKEKSI
          EKYKYVENFGLIDGRLTICT.SCFFAIVALIWDYMHPF.ESKPVLALCVISYFVMMGILTIYTSYKEKSI
Retrocopy EKYKYVENFGLIDGRLTICTLSCFFAIVALIWDYMHPFAESKPVLALCVISYFVMMGILTIYTSYKEKSI

Parental  FLVAHRKDPTGMDPDDIWQLSSSLKRFDDKYTLKLTFISGRTKQQREAEFTKSIAKFFDHSGTLVMDAYE
          FLVAHRKDPTGMDPDDIWQLSSSL.RF.DK.TLKLTF.SGRTKQQREAEFTKS.AKFFDHSGTLVMDAYE
Retrocopy FLVAHRKDPTGMDPDDIWQLSSSLQRFNDK*TLKLTFSSGRTKQQREAEFTKSVAKFFDHSGTLVMDAYE

Parental  PEISRLHD
          PEISRLHD
Retrocopy PEISRLHD

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	0.02 RPM	14.64 RPM
SRP051959_heart	0.02 RPM	13.59 RPM
SRP051959_kidney	0.02 RPM	13.25 RPM
SRP051959_liver	0.04 RPM	23.39 RPM
SRP051959_lung	0.07 RPM	11.75 RPM
SRP051959_lymph_node	0.09 RPM	13.95 RPM
SRP051959_skeletal_muscle	0.04 RPM	16.09 RPM
SRP051959_spleen	0.00 RPM	17.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1929 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1929 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1929 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017127	1 retrocopy	retro_amel_1372,
Choloepus hoffmanni	ENSCHOG00000002974	3 retrocopies	retro_chof_1392, retro_chof_1588, retro_chof_2300,
Callithrix jacchus	ENSCJAG00000015576	2 retrocopies	retro_cjac_1500, retro_cjac_1929 ,
Cavia porcellus	ENSCPOG00000007273	2 retrocopies	retro_cpor_438, retro_cpor_578,
Dipodomys ordii	ENSDORG00000009679	1 retrocopy	retro_dord_423,
Homo sapiens	ENSG00000118363	4 retrocopies	retro_hsap_1488, retro_hsap_3137, retro_hsap_360, retro_hsap_723,
Gorilla gorilla	ENSGGOG00000014500	3 retrocopies	retro_ggor_1141, retro_ggor_372, retro_ggor_610,
Microcebus murinus	ENSMICG00000011153	2 retrocopies	retro_mmur_1566, retro_mmur_656,
Macaca mulatta	ENSMMUG00000010685	1 retrocopy	retro_mmul_26,
Monodelphis domestica	ENSMODG00000007130	2 retrocopies	retro_mdom_1127, retro_mdom_1454,
Mus musculus	ENSMUSG00000035227	1 retrocopy	retro_mmus_2088,
Nomascus leucogenys	ENSNLEG00000016949	2 retrocopies	retro_nleu_1710, retro_nleu_470,
Otolemur garnettii	ENSOGAG00000015621	1 retrocopy	retro_ogar_2649,
Ochotona princeps	ENSOPRG00000014459	2 retrocopies	retro_opri_266, retro_opri_948,
Pongo abelii	ENSPPYG00000003682	4 retrocopies	retro_pabe_1237, retro_pabe_2619, retro_pabe_2817, retro_pabe_625,
Pan troglodytes	ENSPTRG00000004073	1 retrocopy	retro_ptro_1007,
Rattus norvegicus	ENSRNOG00000018164	2 retrocopies	retro_rnor_2078, retro_rnor_2168,
Sarcophilus harrisii	ENSSHAG00000005389	1 retrocopy	retro_shar_787,
Sus scrofa	ENSSSCG00000014850	1 retrocopy	retro_sscr_648,
Ictidomys tridecemlineatus	ENSSTOG00000012647	2 retrocopies	retro_itri_1283, retro_itri_1584,
Tursiops truncatus	ENSTTRG00000005830	3 retrocopies	retro_ttru_1478, retro_ttru_1496, retro_ttru_1867,