RetrogeneDB ID: retro_hsap_273

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:184793506..184793765(+)
• Located in intron of: ENSG00000135842

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGN2
• Ensembl ID: ENSG00000198830
• Aliases: None
• Description: high mobility group nucleosomal binding domain 2 [Source:HGNC Symbol;Acc:4986]

Sequence

>retro_hsap_273
AAAGTCTGAGGGGATGCTCCAAGAGATACAGCCACATTGAAGGATAAACCACAGAGAAGATCAGCAAGGTTGTCTGCTTG
ACCTGCTTCTCCACAGCCAGAACCCAAGCCCCAAAAGGCCCCTGCTAAGAAGGAAGAGAAGGTACGCAGAAGGAAAAAAG
GGAAAGGCTGGCACTGGCAAAGAGGGAAATAATCCTGCAGAAAATGGAGATGCCAGAACAGACCAGGCACAGAAAGCTGA
CGATGCTGGAGATGCCAGG

Alignment

ORF - retro_hsap_273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.71 %
• Parental protein coverage: 95.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKV-PKGKKGKADAGKEGNNPAENG
          K..GDA..D.A..KD.PQRRSARLSA.PA.P.PEPKP.KAPAKK.EKV...GKKGKA..GKEGNNPAENG
Retrocopy KV*GDAPRDTATLKDKPQRRSARLSA*PASPQPEPKPQKAPAKKEEKV>AEGKKGKAGTGKEGNNPAENG

Parental  DAKTDQAQKAEGAGDAK
          DA.TDQAQKA..AGDA.
Retrocopy DARTDQAQKADDAGDAR

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	96.51 RPM
bodymap2_adrenal	0.04 RPM	86.18 RPM
bodymap2_brain	0.00 RPM	48.10 RPM
bodymap2_breast	0.16 RPM	101.62 RPM
bodymap2_colon	0.00 RPM	110.02 RPM
bodymap2_heart	0.20 RPM	27.21 RPM
bodymap2_kidney	0.00 RPM	79.95 RPM
bodymap2_liver	0.00 RPM	24.52 RPM
bodymap2_lung	0.09 RPM	99.30 RPM
bodymap2_lymph_node	0.00 RPM	53.10 RPM
bodymap2_ovary	0.00 RPM	163.04 RPM
bodymap2_prostate	0.28 RPM	155.86 RPM
bodymap2_skeletal_muscle	0.11 RPM	80.99 RPM
bodymap2_testis	0.02 RPM	95.68 RPM
bodymap2_thyroid	0.02 RPM	157.77 RPM
bodymap2_white_blood_cells	0.00 RPM	182.92 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_273 was not detected

EST

No EST(s) were mapped for retro_hsap_273 retrocopy.

TSS

No TSS is located nearby retro_hsap_273 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: AGAATGACGTCTAGACCGAC (20 nt long)
• Reverse primer: GTGTCAGGTCCCAACAGGTC (20 nt long)
• Anneling temperature: 58 °C
• (Expected) product size: 741
• Electrophoresis gel image:
• Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Homology

Retrocopy orthology:

Retrocopy retro_hsap_273 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_229
Pongo abelii	retro_pabe_396

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 148 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000012812	3 retrocopies	retro_fcat_1842, retro_fcat_4, retro_fcat_530,
Homo sapiens	ENSG00000198830	51 retrocopies	retro_hsap_100, retro_hsap_114, retro_hsap_1208, retro_hsap_1368, retro_hsap_1395, retro_hsap_1427, retro_hsap_1471, retro_hsap_1492, retro_hsap_1512, retro_hsap_1517, retro_hsap_1518, retro_hsap_1586, retro_hsap_1670, retro_hsap_1684, retro_hsap_1787, retro_hsap_1834, retro_hsap_1931, retro_hsap_1934, retro_hsap_2082, retro_hsap_2116, retro_hsap_2296, retro_hsap_2309, retro_hsap_233, retro_hsap_2564, retro_hsap_2592, retro_hsap_2728, retro_hsap_273 , retro_hsap_2755, retro_hsap_2779, retro_hsap_2849, retro_hsap_2914, retro_hsap_318, retro_hsap_3189, retro_hsap_3339, retro_hsap_3372, retro_hsap_3412, retro_hsap_3515, retro_hsap_3616, retro_hsap_3755, retro_hsap_3896, retro_hsap_4124, retro_hsap_4138, retro_hsap_4297, retro_hsap_4791, retro_hsap_4914, retro_hsap_601, retro_hsap_688, retro_hsap_689, retro_hsap_718, retro_hsap_793, retro_hsap_849,
Gorilla gorilla	ENSGGOG00000000971	11 retrocopies	retro_ggor_114, retro_ggor_146, retro_ggor_162, retro_ggor_166, retro_ggor_182, retro_ggor_186, retro_ggor_197, retro_ggor_23, retro_ggor_38, retro_ggor_40, retro_ggor_54,
Macropus eugenii	ENSMEUG00000010966	8 retrocopies	retro_meug_1178, retro_meug_126, retro_meug_1859, retro_meug_1910, retro_meug_1997, retro_meug_248, retro_meug_369, retro_meug_76,
Mus musculus	ENSMUSG00000003038	2 retrocopies	retro_mmus_202, retro_mmus_2582,
Otolemur garnettii	ENSOGAG00000032571	14 retrocopies	retro_ogar_1438, retro_ogar_1445, retro_ogar_1603, retro_ogar_1668, retro_ogar_1687, retro_ogar_1998, retro_ogar_2097, retro_ogar_2210, retro_ogar_2231, retro_ogar_2424, retro_ogar_287, retro_ogar_2989, retro_ogar_3411, retro_ogar_52,
Pan troglodytes	ENSPTRG00000000386	54 retrocopies	retro_ptro_1011, retro_ptro_1024, retro_ptro_1026, retro_ptro_1027, retro_ptro_1040, retro_ptro_1053, retro_ptro_1067, retro_ptro_1094, retro_ptro_1197, retro_ptro_1235, retro_ptro_128, retro_ptro_1291, retro_ptro_1292, retro_ptro_1495, retro_ptro_1516, retro_ptro_1532, retro_ptro_1549, retro_ptro_1625, retro_ptro_1633, retro_ptro_1837, retro_ptro_1844, retro_ptro_1863, retro_ptro_1880, retro_ptro_1929, retro_ptro_1970, retro_ptro_203, retro_ptro_2255, retro_ptro_229, retro_ptro_2292, retro_ptro_2317, retro_ptro_2387, retro_ptro_2445, retro_ptro_2461, retro_ptro_2549, retro_ptro_257, retro_ptro_2650, retro_ptro_2801, retro_ptro_2812, retro_ptro_2840, retro_ptro_2913, retro_ptro_2970, retro_ptro_3187, retro_ptro_3276, retro_ptro_445, retro_ptro_493, retro_ptro_495, retro_ptro_512, retro_ptro_543, retro_ptro_552, retro_ptro_59, retro_ptro_590, retro_ptro_827, retro_ptro_939, retro_ptro_958,
Tursiops truncatus	ENSTTRG00000005681	5 retrocopies	retro_ttru_1392, retro_ttru_1443, retro_ttru_3, retro_ttru_345, retro_ttru_788,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.03 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	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 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	0.04 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 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	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 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).