RetrogeneDB ID: retro_hsap_1418

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:55861692..55861951(-)
• Located in intron of: ENSG00000126775

Retrocopy information

• Ensembl ID: ENSG00000259318
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HMGN1
• Ensembl ID: ENSG00000205581
• Aliases: HMGN1, HMG14
• Description: high mobility group nucleosome binding domain 1 [Source:HGNC Symbol;Acc:4984]

Sequence

>retro_hsap_1418
ATGCCCAAGAGGAAGGTCAGCTCCACTGAATGGGCCACAGAGGAAGAGCCCAAGAGGAGATCGGCACGCTTATCAGCTGA
ACCTGCTCCTGCAAAAGTGGAAACGAAGCTGAGAAAGCAGCAGGAAAGGATAAATCTTCAGACAAAAAAGTGCAAACAAA
AGGGAAAAGGGGAGCAAAGGGGGAAAAGTCAGAAGTGGCTAACCAAGAAACTGAAGATTTACCTGCAGAAAACAAGAAAC
TAAAACTGAGGAGAGCCCC

Alignment

ORF - retro_hsap_1418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.56 %
• Parental protein coverage: 87. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKRKVSSAEGAAKEEPKRRSARLSAKP-PAKVEAK-PKKAAAKDKSSDKKVQTKGKRGAKGKQAEVANQ
          MPKRKVSS.E.A..EEPKRRSARLSA.P.PAKVE.K...KAA.KDKSS.................EVANQ
Retrocopy MPKRKVSSTEWATEEEPKRRSARLSAEPAPAKVETK<AEKAAGKDKSSXXXXXXXXXXXXXXXXXEVANQ

Parental  ETKEDLPAEN-GETKTEESP
          ET.EDLPAEN..ETKTEESP
Retrocopy ET-EDLPAEN<QETKTEESP

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	0.28 RPM	62.20 RPM
bodymap2_adrenal	1.43 RPM	100.83 RPM
bodymap2_brain	0.61 RPM	28.88 RPM
bodymap2_breast	0.25 RPM	67.18 RPM
bodymap2_colon	0.00 RPM	68.29 RPM
bodymap2_heart	0.24 RPM	23.08 RPM
bodymap2_kidney	0.15 RPM	94.80 RPM
bodymap2_liver	0.04 RPM	31.52 RPM
bodymap2_lung	0.07 RPM	105.05 RPM
bodymap2_lymph_node	0.00 RPM	69.48 RPM
bodymap2_ovary	0.35 RPM	151.40 RPM
bodymap2_prostate	0.12 RPM	88.92 RPM
bodymap2_skeletal_muscle	0.00 RPM	6.15 RPM
bodymap2_testis	0.13 RPM	75.70 RPM
bodymap2_thyroid	0.36 RPM	114.83 RPM
bodymap2_white_blood_cells	0.12 RPM	99.29 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1418 was not detected

EST

No EST(s) were mapped for retro_hsap_1418 retrocopy.

TSS

No TSS is located nearby retro_hsap_1418 retrocopy 5' end.

Lab

retro_hsap_1418 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1418 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_970
Pongo abelii	retro_pabe_1172

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 129 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014100	11 retrocopies	retro_amel_1103, retro_amel_1157, retro_amel_1307, retro_amel_1378, retro_amel_1580, retro_amel_1839, retro_amel_349, retro_amel_352, retro_amel_408, retro_amel_439, retro_amel_670,
Bos taurus	ENSBTAG00000018768	12 retrocopies	retro_btau_1178, retro_btau_1475, retro_btau_1560, retro_btau_1746, retro_btau_1801, retro_btau_388, retro_btau_504, retro_btau_572, retro_btau_607, retro_btau_617, retro_btau_897, retro_btau_928,
Cavia porcellus	ENSCPOG00000002336	7 retrocopies	retro_cpor_1129, retro_cpor_1389, retro_cpor_334, retro_cpor_349, retro_cpor_4, retro_cpor_884, retro_cpor_949,
Equus caballus	ENSECAG00000019029	5 retrocopies	retro_ecab_1130, retro_ecab_285, retro_ecab_362, retro_ecab_800, retro_ecab_848,
Homo sapiens	ENSG00000205581	7 retrocopies	retro_hsap_1097, retro_hsap_1418 , retro_hsap_1581, retro_hsap_1758, retro_hsap_1874, retro_hsap_3370, retro_hsap_762,
Monodelphis domestica	ENSMODG00000020972	5 retrocopies	retro_mdom_1085, retro_mdom_109, retro_mdom_284, retro_mdom_755, retro_mdom_88,
Otolemur garnettii	ENSOGAG00000010329	35 retrocopies	retro_ogar_1062, retro_ogar_1186, retro_ogar_1245, retro_ogar_1304, retro_ogar_1355, retro_ogar_1437, retro_ogar_1527, retro_ogar_1529, retro_ogar_175, retro_ogar_1812, retro_ogar_1901, retro_ogar_1932, retro_ogar_2057, retro_ogar_2311, retro_ogar_2325, retro_ogar_2522, retro_ogar_2523, retro_ogar_266, retro_ogar_2712, retro_ogar_2729, retro_ogar_278, retro_ogar_2913, retro_ogar_2964, retro_ogar_3095, retro_ogar_3133, retro_ogar_3138, retro_ogar_3155, retro_ogar_333, retro_ogar_3354, retro_ogar_370, retro_ogar_393, retro_ogar_657, retro_ogar_699, retro_ogar_723, retro_ogar_958,
Pongo abelii	ENSPPYG00000011426	25 retrocopies	retro_pabe_1066, retro_pabe_1149, retro_pabe_1172, retro_pabe_1190, retro_pabe_123, retro_pabe_1264, retro_pabe_1302, retro_pabe_1504, retro_pabe_1604, retro_pabe_1842, retro_pabe_2152, retro_pabe_2211, retro_pabe_2284, retro_pabe_2380, retro_pabe_251, retro_pabe_2518, retro_pabe_2771, retro_pabe_3086, retro_pabe_3648, retro_pabe_3825, retro_pabe_504, retro_pabe_698, retro_pabe_699, retro_pabe_702, retro_pabe_760,
Pan troglodytes	ENSPTRG00000031426	22 retrocopies	retro_ptro_1256, retro_ptro_1299, retro_ptro_1301, retro_ptro_1454, retro_ptro_1556, retro_ptro_1740, retro_ptro_1821, retro_ptro_1830, retro_ptro_2058, retro_ptro_2290, retro_ptro_2559, retro_ptro_2716, retro_ptro_3119, retro_ptro_3278, retro_ptro_363, retro_ptro_463, retro_ptro_586, retro_ptro_61, retro_ptro_637, retro_ptro_696, retro_ptro_970, retro_ptro_980,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.39 RPM
CEU_NA11843	0.17 RPM
CEU_NA11930	0.29 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.41 RPM
CEU_NA12760	0.13 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.27 RPM
CEU_NA12873	0.57 RPM
FIN_HG00183	0.16 RPM
FIN_HG00277	0.18 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.27 RPM
FIN_HG00328	0.19 RPM
FIN_HG00338	0.19 RPM
FIN_HG00349	0.09 RPM
FIN_HG00375	0.07 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.11 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.24 RPM
GBR_HG00119	0.43 RPM
GBR_HG00131	0.52 RPM
GBR_HG00133	0.41 RPM
GBR_HG00134	0.26 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.36 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.36 RPM
TSI_NA20518	0.14 RPM
TSI_NA20532	0.20 RPM
TSI_NA20538	0.18 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.35 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.10 RPM
TSI_NA20798	0.09 RPM
YRI_NA18870	0.34 RPM
YRI_NA18907	0.35 RPM
YRI_NA18916	0.32 RPM
YRI_NA19093	0.23 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.10 RPM
YRI_NA19118	0.12 RPM
YRI_NA19213	0.24 RPM
YRI_NA19214	0.25 RPM
YRI_NA19223	0.22 RPM

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Indel association:

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