RetrogeneDB ID: retro_hsap_2177

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:172349417..172349629(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000234061
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UFM1
• Ensembl ID: ENSG00000120686
• Aliases: UFM1, BM-002, C13orf20
• Description: ubiquitin-fold modifier 1 [Source:HGNC Symbol;Acc:20597]

Sequence

>retro_hsap_2177
TCAAAGCTTTCCTTTAAGATCACTCTGACGTCCGACCTGCGGCTGCTGTACAAAGTACTCAGTGTTCCTGAAAGTACACC
TTTCACAGCAGTCTTAAAGATTGCAGCAGAATAATTTAAAGTCCTGCTGCAACAAGTGCAATTACTGCCAGTGATGGAAT
ACAAATAAATTCTGCACAGACTGCTGGTTCAGAACTACAAAGTATGCCTGGA

Alignment

ORF - retro_hsap_2177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.39 %
• Parental protein coverage: 87.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKV-PAATSAIITNDGIGINPAQTAGEYLKTH
          SK.SFKITLTSD.RL.YKVLSVPESTPFTAVLK.AAE.FKV.PAATSAI...DGI.IN.AQTAG..L...
Retrocopy SKLSFKITLTSDLRLLYKVLSVPESTPFTAVLKIAAE*FKV<PAATSAITASDGIQINSAQTAGSELQSM

Parental  RG
          .G
Retrocopy PG

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	98.24 RPM
bodymap2_adrenal	0.00 RPM	100.98 RPM
bodymap2_brain	0.00 RPM	97.96 RPM
bodymap2_breast	0.00 RPM	109.67 RPM
bodymap2_colon	0.00 RPM	74.69 RPM
bodymap2_heart	0.00 RPM	38.51 RPM
bodymap2_kidney	0.00 RPM	117.65 RPM
bodymap2_liver	0.00 RPM	68.69 RPM
bodymap2_lung	0.00 RPM	105.36 RPM
bodymap2_lymph_node	0.00 RPM	96.63 RPM
bodymap2_ovary	0.00 RPM	104.11 RPM
bodymap2_prostate	0.07 RPM	87.28 RPM
bodymap2_skeletal_muscle	0.00 RPM	28.79 RPM
bodymap2_testis	0.15 RPM	80.24 RPM
bodymap2_thyroid	0.04 RPM	107.38 RPM
bodymap2_white_blood_cells	0.14 RPM	75.31 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2177 was not detected

EST

No EST(s) were mapped for retro_hsap_2177 retrocopy.

TSS

No TSS is located nearby retro_hsap_2177 retrocopy 5' end.

Lab

retro_hsap_2177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2177 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1660
Pongo abelii	retro_pabe_2061
Macaca mulatta	retro_mmul_908
Callithrix jacchus	retro_cjac_2807

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006026	1 retrocopy	retro_cfam_1785,
Callithrix jacchus	ENSCJAG00000017903	4 retrocopies	retro_cjac_1489, retro_cjac_2545, retro_cjac_2807, retro_cjac_2872,
Equus caballus	ENSECAG00000014564	3 retrocopies	retro_ecab_293, retro_ecab_353, retro_ecab_392,
Erinaceus europaeus	ENSEEUG00000008471	1 retrocopy	retro_eeur_187,
Homo sapiens	ENSG00000120686	4 retrocopies	retro_hsap_1825, retro_hsap_2177 , retro_hsap_4098, retro_hsap_4767,
Gorilla gorilla	ENSGGOG00000026214	3 retrocopies	retro_ggor_2168, retro_ggor_2750, retro_ggor_2970,
Macropus eugenii	ENSMEUG00000001660	2 retrocopies	retro_meug_1215, retro_meug_1615,
Microcebus murinus	ENSMICG00000008048	1 retrocopy	retro_mmur_1161,
Macaca mulatta	ENSMMUG00000014990	3 retrocopies	retro_mmul_1253, retro_mmul_2542, retro_mmul_908,
Mus musculus	ENSMUSG00000027746	2 retrocopies	retro_mmus_2246, retro_mmus_2311,
Nomascus leucogenys	ENSNLEG00000002556	3 retrocopies	retro_nleu_2973, retro_nleu_305, retro_nleu_567,
Otolemur garnettii	ENSOGAG00000007023	6 retrocopies	retro_ogar_2303, retro_ogar_2304, retro_ogar_2534, retro_ogar_2571, retro_ogar_617, retro_ogar_948,
Pongo abelii	ENSPPYG00000005293	4 retrocopies	retro_pabe_1492, retro_pabe_2061, retro_pabe_3354, retro_pabe_3710,
Pan troglodytes	ENSPTRG00000040645	4 retrocopies	retro_ptro_1169, retro_ptro_1660, retro_ptro_2779, retro_ptro_3174,
Rattus norvegicus	ENSRNOG00000038176	2 retrocopies	retro_rnor_2201, retro_rnor_2202,
Sus scrofa	ENSSSCG00000021299	1 retrocopy	retro_sscr_584,
Ictidomys tridecemlineatus	ENSSTOG00000016449	2 retrocopies	retro_itri_1685, retro_itri_1746,
Tarsius syrichta	ENSTSYG00000011105	1 retrocopy	retro_tsyr_1979,
Tursiops truncatus	ENSTTRG00000015482	2 retrocopies	retro_ttru_1434, retro_ttru_518,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.07 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.06 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.09 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.08 RPM
GBR_HG00099	0.17 RPM
GBR_HG00111	0.06 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.07 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.11 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.06 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.04 RPM

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Indel association:

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