RetrogeneDB ID: retro_hsap_1968

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 19:14600199..14600421(+)
• Located in intron of: ENSG00000123159

Retrocopy information

• Ensembl ID: ENSG00000224543
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPG
• Ensembl ID: ENSG00000143977
• Aliases: SNRPG, SMG, Sm-G
• Description: small nuclear ribonucleoprotein polypeptide G [Source:HGNC Symbol;Acc:11163]

Sequence

>retro_hsap_1968
ATGAGCAAAGCTCACCCTCCTGAGTTGAAAAAATTTACGGACAAGAAGTTTTCATTGAAATTAAATGGTGGCAGACATGT
CCAAGGAATATTGCGGGGATTTGATCCCTTTATGAACCTTGTGATAGATGAATGTGTGGAGATGGCGACTAGTGGACAAC
AGAAAAATATTGGAATGGTGGAAATACGAGGAAATAGTATCATCATGTTAGAAGCCTTGGAA

Alignment

ORF - retro_hsap_1968 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.59 %
• Parental protein coverage: 97.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIML
          MSKAHPPELKKF.DKK.SLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQ.NIGMV.IRGNSIIML
Retrocopy MSKAHPPELKKFTDKKFSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQKNIGMVEIRGNSIIML

Parental  EALE
          EALE
Retrocopy EALE

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	0.38 RPM	12.22 RPM
bodymap2_adrenal	1.47 RPM	21.70 RPM
bodymap2_brain	1.99 RPM	10.64 RPM
bodymap2_breast	0.93 RPM	16.52 RPM
bodymap2_colon	0.12 RPM	19.76 RPM
bodymap2_heart	0.15 RPM	22.97 RPM
bodymap2_kidney	0.41 RPM	24.65 RPM
bodymap2_liver	0.19 RPM	27.69 RPM
bodymap2_lung	0.16 RPM	42.72 RPM
bodymap2_lymph_node	0.00 RPM	36.75 RPM
bodymap2_ovary	0.54 RPM	22.19 RPM
bodymap2_prostate	0.10 RPM	26.74 RPM
bodymap2_skeletal_muscle	0.02 RPM	24.21 RPM
bodymap2_testis	0.34 RPM	31.73 RPM
bodymap2_thyroid	0.90 RPM	27.27 RPM
bodymap2_white_blood_cells	0.00 RPM	29.57 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1968 was not detected

EST

No EST(s) were mapped for retro_hsap_1968 retrocopy.

TSS

No TSS is located nearby retro_hsap_1968 retrocopy 5' end.

Lab

retro_hsap_1968 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1968 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1314

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 219 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032595	14 retrocopies	retro_cfam_1060, retro_cfam_1458, retro_cfam_1871, retro_cfam_1984, retro_cfam_2210, retro_cfam_279, retro_cfam_306, retro_cfam_313, retro_cfam_407, retro_cfam_505, retro_cfam_817, retro_cfam_956, retro_cfam_967, retro_cfam_991,
Callithrix jacchus	ENSCJAG00000019313	18 retrocopies	retro_cjac_1034, retro_cjac_1227, retro_cjac_1398, retro_cjac_149, retro_cjac_1897, retro_cjac_223, retro_cjac_2419, retro_cjac_2431, retro_cjac_2658, retro_cjac_2795, retro_cjac_3246, retro_cjac_3314, retro_cjac_4078, retro_cjac_547, retro_cjac_763, retro_cjac_796, retro_cjac_897, retro_cjac_998,
Cavia porcellus	ENSCPOG00000025022	6 retrocopies	retro_cpor_1323, retro_cpor_145, retro_cpor_531, retro_cpor_573, retro_cpor_673, retro_cpor_843,
Equus caballus	ENSECAG00000019989	5 retrocopies	retro_ecab_1080, retro_ecab_197, retro_ecab_376, retro_ecab_410, retro_ecab_693,
Felis catus	ENSFCAG00000008118	8 retrocopies	retro_fcat_1006, retro_fcat_1092, retro_fcat_1248, retro_fcat_1467, retro_fcat_1893, retro_fcat_562, retro_fcat_82, retro_fcat_90,
Homo sapiens	ENSG00000143977	12 retrocopies	retro_hsap_1187, retro_hsap_1267, retro_hsap_1413, retro_hsap_1784, retro_hsap_1943, retro_hsap_1968 , retro_hsap_2139, retro_hsap_2241, retro_hsap_2392, retro_hsap_296, retro_hsap_3786, retro_hsap_810,
Loxodonta africana	ENSLAFG00000002301	3 retrocopies	retro_lafr_428, retro_lafr_559, retro_lafr_887,
Microcebus murinus	ENSMICG00000015369	10 retrocopies	retro_mmur_1419, retro_mmur_1468, retro_mmur_1550, retro_mmur_265, retro_mmur_395, retro_mmur_59, retro_mmur_595, retro_mmur_625, retro_mmur_735, retro_mmur_901,
Myotis lucifugus	ENSMLUG00000026490	3 retrocopies	retro_mluc_273, retro_mluc_46, retro_mluc_731,
Macaca mulatta	ENSMMUG00000007961	3 retrocopies	retro_mmul_1021, retro_mmul_2048, retro_mmul_300,
Monodelphis domestica	ENSMODG00000011528	1 retrocopy	retro_mdom_1945,
Mustela putorius furo	ENSMPUG00000007221	2 retrocopies	retro_mputfur_100, retro_mputfur_114,
Mus musculus	ENSMUSG00000057278	1 retrocopy	retro_mmus_186,
Nomascus leucogenys	ENSNLEG00000010182	1 retrocopy	retro_nleu_93,
Oryctolagus cuniculus	ENSOCUG00000011214	2 retrocopies	retro_ocun_1032, retro_ocun_57,
Otolemur garnettii	ENSOGAG00000015300	13 retrocopies	retro_ogar_1138, retro_ogar_1691, retro_ogar_1982, retro_ogar_2533, retro_ogar_2626, retro_ogar_2696, retro_ogar_2787, retro_ogar_3149, retro_ogar_3386, retro_ogar_351, retro_ogar_638, retro_ogar_745, retro_ogar_836,
Pongo abelii	ENSPPYG00000012324	14 retrocopies	retro_pabe_1054, retro_pabe_1078, retro_pabe_1079, retro_pabe_1169, retro_pabe_1188, retro_pabe_1465, retro_pabe_1603, retro_pabe_1728, retro_pabe_1929, retro_pabe_2041, retro_pabe_2160, retro_pabe_3093, retro_pabe_495, retro_pabe_95,
Pan troglodytes	ENSPTRG00000012029	11 retrocopies	retro_ptro_1194, retro_ptro_1297, retro_ptro_1314, retro_ptro_1565, retro_ptro_1585, retro_ptro_243, retro_ptro_2568, retro_ptro_563, retro_ptro_814, retro_ptro_867, retro_ptro_967,
Pteropus vampyrus	ENSPVAG00000004855	3 retrocopies	retro_pvam_612, retro_pvam_613, retro_pvam_666,
Rattus norvegicus	ENSRNOG00000016507	1 retrocopy	retro_rnor_409,
Ictidomys tridecemlineatus	ENSSTOG00000008654	11 retrocopies	retro_itri_1116, retro_itri_1260, retro_itri_128, retro_itri_1395, retro_itri_1871, retro_itri_280, retro_itri_353, retro_itri_572, retro_itri_589, retro_itri_910, retro_itri_947,
Tupaia belangeri	ENSTBEG00000017381	66 retrocopies	retro_tbel_1010, retro_tbel_1076, retro_tbel_1114, retro_tbel_1133, retro_tbel_1161, retro_tbel_1164, retro_tbel_1174, retro_tbel_121, retro_tbel_1288, retro_tbel_1448, retro_tbel_1461, retro_tbel_147, retro_tbel_1478, retro_tbel_149, retro_tbel_164, retro_tbel_1654, retro_tbel_1887, retro_tbel_1939, retro_tbel_1944, retro_tbel_1965, retro_tbel_1966, retro_tbel_1997, retro_tbel_2001, retro_tbel_2143, retro_tbel_217, retro_tbel_236, retro_tbel_239, retro_tbel_241, retro_tbel_2454, retro_tbel_2462, retro_tbel_2572, retro_tbel_2664, retro_tbel_2941, retro_tbel_3098, retro_tbel_3379, retro_tbel_3385, retro_tbel_343, retro_tbel_347, retro_tbel_3495, retro_tbel_3559, retro_tbel_3603, retro_tbel_362, retro_tbel_3699, retro_tbel_3980, retro_tbel_3981, retro_tbel_3983, retro_tbel_4010, retro_tbel_4011, retro_tbel_4177, retro_tbel_4196, retro_tbel_43, retro_tbel_4399, retro_tbel_4442, retro_tbel_4505, retro_tbel_4549, retro_tbel_4609, retro_tbel_465, retro_tbel_489, retro_tbel_697, retro_tbel_726, retro_tbel_736, retro_tbel_805, retro_tbel_921, retro_tbel_93, retro_tbel_936, retro_tbel_947,
Tarsius syrichta	ENSTSYG00000005729	11 retrocopies	retro_tsyr_1202, retro_tsyr_134, retro_tsyr_1440, retro_tsyr_1592, retro_tsyr_1747, retro_tsyr_2038, retro_tsyr_222, retro_tsyr_287, retro_tsyr_322, retro_tsyr_431, retro_tsyr_698,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	1.20 RPM
CEU_NA11843	1.59 RPM
CEU_NA11930	0.95 RPM
CEU_NA12004	1.56 RPM
CEU_NA12400	0.67 RPM
CEU_NA12751	0.78 RPM
CEU_NA12760	1.17 RPM
CEU_NA12827	0.52 RPM
CEU_NA12872	0.73 RPM
CEU_NA12873	1.12 RPM
FIN_HG00183	0.82 RPM
FIN_HG00277	1.40 RPM
FIN_HG00315	0.97 RPM
FIN_HG00321	1.00 RPM
FIN_HG00328	0.85 RPM
FIN_HG00338	1.30 RPM
FIN_HG00349	1.65 RPM
FIN_HG00375	0.86 RPM
FIN_HG00377	1.66 RPM
FIN_HG00378	1.13 RPM
GBR_HG00099	0.81 RPM
GBR_HG00111	1.66 RPM
GBR_HG00114	1.63 RPM
GBR_HG00119	1.27 RPM
GBR_HG00131	0.72 RPM
GBR_HG00133	1.16 RPM
GBR_HG00134	0.85 RPM
GBR_HG00137	0.71 RPM
GBR_HG00142	1.08 RPM
GBR_HG00143	1.28 RPM
TSI_NA20512	1.64 RPM
TSI_NA20513	0.97 RPM
TSI_NA20518	0.89 RPM
TSI_NA20532	1.22 RPM
TSI_NA20538	0.83 RPM
TSI_NA20756	1.83 RPM
TSI_NA20765	1.60 RPM
TSI_NA20771	1.13 RPM
TSI_NA20786	1.23 RPM
TSI_NA20798	1.65 RPM
YRI_NA18870	0.98 RPM
YRI_NA18907	1.01 RPM
YRI_NA18916	1.20 RPM
YRI_NA19093	1.09 RPM
YRI_NA19099	1.28 RPM
YRI_NA19114	0.97 RPM
YRI_NA19118	1.55 RPM
YRI_NA19213	0.77 RPM
YRI_NA19214	0.86 RPM
YRI_NA19223	1.07 RPM

---

Indel association:

The presence of retro_hsap_1968 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_1968 presence in various populations. Based on Kabza et al. 2015 (PubMed).

#	Indel coordinates	AFR, African			AMR, Ad Mixed American			EUR, European					EAS, East Asian
		ASW	YRI	LWK	MXL	PUR	CLM	CEU	IBS	GBR	FIN	TSI	JPT	CHB	CHS
1.	19:14599517..14601700	100	100	98.97	100	99.09	100	100	100	100	100	100	100	100	100

---

Indel #1, located at the genomic coordinates 19:14599517..14601700.