RetrogeneDB ID: retro_hsap_3137

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:816460..816803(+)
• Located in intron of: ENSG00000188818

Retrocopy information

• Ensembl ID: ENSG00000247872
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SPCS2
• Ensembl ID: ENSG00000118363
• Aliases: None
• Description: signal peptidase complex subunit 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28962]

Sequence

>retro_hsap_3137
ATGGCGGCAGCAGCTGCACGGGCGGGAGGGGGGCGGTAGCGCAGGCGGTGGTGGGGTTGGCGGGGGTTCCAGCTGCGGGA
CAGGCAGTGGCCGTAGCGGCATGTGGATAAGTCGAAGATAAGTGATATGCCTGGAAAAACGGACAAGTGGGATGGATCAG
CTGTGAAAAACTCTGGATGATTCTGCCAAAAAGATACTTCTGGAAAAATACAAATACGTGGAGAATTTTTGTCTAATTGA
CGGTCACCTCACCATCTGTACAATCTCCTGTTGCTTTGCCATAGTGGCTGTGATTTGGGATTATATGCATCCCTTTCCAG
AGTCCAAGCCCGTTTTGGCTTTG

Alignment

ORF - retro_hsap_3137 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.17 %
• Parental protein coverage: 51.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAAAVQ-GGRS-GGSGGCSGAGGASNCGTGSGRSGL-LDKWKIDDKPVKIDKWDGSAVKNS-LDDSAKK
          MAAAA...GGR..GGS.G..G.GG.S.CGTGSGRSG...DK.KI.D.P.K.DKWDGSAVKNS..D...K.
Retrocopy MAAAAAR<GGRG<GGSAGGGGVGGGSSCGTGSGRSGM<VDKSKISDMPGKTDKWDGSAVKNS>DDSAKKI

Parental  VLLEKYKYVENFGLIDGRLTICTISCFFAIVALIWDYMHPFPESKPVLAL
          .L.EKYKYVENF.LIDG.LTICTISC.FAIVA.IWDYMHPFPESKPVLAL
Retrocopy LL-EKYKYVENFCLIDGHLTICTISCCFAIVAVIWDYMHPFPESKPVLAL

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
bodymap2_adipose	0.00 RPM	25.26 RPM
bodymap2_adrenal	0.00 RPM	37.62 RPM
bodymap2_brain	0.00 RPM	31.10 RPM
bodymap2_breast	0.00 RPM	26.15 RPM
bodymap2_colon	0.00 RPM	45.21 RPM
bodymap2_heart	0.02 RPM	17.43 RPM
bodymap2_kidney	0.00 RPM	60.72 RPM
bodymap2_liver	0.00 RPM	43.16 RPM
bodymap2_lung	0.00 RPM	38.29 RPM
bodymap2_lymph_node	0.00 RPM	62.44 RPM
bodymap2_ovary	0.00 RPM	37.28 RPM
bodymap2_prostate	0.00 RPM	45.27 RPM
bodymap2_skeletal_muscle	0.00 RPM	17.41 RPM
bodymap2_testis	0.00 RPM	40.89 RPM
bodymap2_thyroid	0.00 RPM	41.13 RPM
bodymap2_white_blood_cells	0.00 RPM	44.16 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3137 was not detected

EST

No EST(s) were mapped for retro_hsap_3137 retrocopy.

TSS

No TSS is located nearby retro_hsap_3137 retrocopy 5' end.

Lab

retro_hsap_3137 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3137 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2619

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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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).