RetrogeneDB ID: retro_hsap_2007

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 19:49778375..49778659(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000235555
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SUMO1
• Ensembl ID: ENSG00000116030
• Aliases: SUMO1, DAP1, GMP1, OFC10, PIC1, SENP2, SMT3, SMT3C, SMT3H3, UBL1
• Description: small ubiquitin-like modifier 1 [Source:HGNC Symbol;Acc:12502]

Sequence

>retro_hsap_2007
ATGTCTGACCAGGAGGCAAAACCTTCAACTGAGGACTTGGGGGATAAGAAGGAAGGTGAATATATTAAACTCAAAGTCAC
TGGACAGGATAGCAGTGAGATTCACTTCAAAGTGAAAATGACAACACATCTCAAGAAACTCAAAGAATCATACTGTCAAA
GACAGGGTATTCCAATGAATCCACTCGGTTTCTCTTTGAGGGTCAGAGAATTGCTGATAATCATACTCCAAAAGAACTGG
GAATGGAGGAAGAAGATGTGATTGAAGTTTATCAGGAACAAACG

Alignment

ORF - retro_hsap_2007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.83 %
• Parental protein coverage: 94.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMN-SLRFLFEGQ
          MSDQEAKPSTEDLGDKKEGEYIKLKV.GQDSSEIHFKVKMTTHLKKLKESYCQRQG.PMN.S.RFLFEGQ
Retrocopy MSDQEAKPSTEDLGDKKEGEYIKLKVTGQDSSEIHFKVKMTTHLKKLKESYCQRQGIPMN<STRFLFEGQ

Parental  RIADNHTPKELGMEEEDVIEVYQEQT
          RIADNHTPKELGMEEEDVIEVYQEQT
Retrocopy RIADNHTPKELGMEEEDVIEVYQEQT

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	0.02 RPM	76.37 RPM
bodymap2_adrenal	0.27 RPM	80.16 RPM
bodymap2_brain	0.02 RPM	123.90 RPM
bodymap2_breast	0.02 RPM	92.84 RPM
bodymap2_colon	0.02 RPM	133.61 RPM
bodymap2_heart	0.00 RPM	46.89 RPM
bodymap2_kidney	0.04 RPM	100.63 RPM
bodymap2_liver	0.00 RPM	65.93 RPM
bodymap2_lung	0.00 RPM	95.60 RPM
bodymap2_lymph_node	0.00 RPM	67.65 RPM
bodymap2_ovary	0.02 RPM	88.10 RPM
bodymap2_prostate	0.00 RPM	91.76 RPM
bodymap2_skeletal_muscle	0.00 RPM	39.67 RPM
bodymap2_testis	0.04 RPM	126.82 RPM
bodymap2_thyroid	0.00 RPM	123.23 RPM
bodymap2_white_blood_cells	0.00 RPM	87.47 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2007 was not detected

EST

No EST(s) were mapped for retro_hsap_2007 retrocopy.

TSS

No TSS is located nearby retro_hsap_2007 retrocopy 5' end.

Lab

retro_hsap_2007 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2007 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1451

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009859	6 retrocopies	retro_btau_112, retro_btau_1512, retro_btau_1705, retro_btau_357, retro_btau_363, retro_btau_499,
Canis familiaris	ENSCAFG00000012431	8 retrocopies	retro_cfam_1226, retro_cfam_1253, retro_cfam_139, retro_cfam_1815, retro_cfam_1912, retro_cfam_2048, retro_cfam_386, retro_cfam_985,
Callithrix jacchus	ENSCJAG00000004961	3 retrocopies	retro_cjac_1686, retro_cjac_1932, retro_cjac_2610,
Cavia porcellus	ENSCPOG00000012143	1 retrocopy	retro_cpor_1279,
Equus caballus	ENSECAG00000024693	4 retrocopies	retro_ecab_199, retro_ecab_365, retro_ecab_570, retro_ecab_935,
Felis catus	ENSFCAG00000031005	6 retrocopies	retro_fcat_1520, retro_fcat_218, retro_fcat_26, retro_fcat_472, retro_fcat_6, retro_fcat_862,
Homo sapiens	ENSG00000116030	5 retrocopies	retro_hsap_2007 , retro_hsap_240, retro_hsap_2489, retro_hsap_262, retro_hsap_897,
Homo sapiens	ENSG00000184900	4 retrocopies	retro_hsap_1675, retro_hsap_1841, retro_hsap_3672, retro_hsap_4103,
Homo sapiens	ENSG00000188612	2 retrocopies	retro_hsap_4036, retro_hsap_4095,
Myotis lucifugus	ENSMLUG00000007504	2 retrocopies	retro_mluc_1346, retro_mluc_188,
Mustela putorius furo	ENSMPUG00000000335	2 retrocopies	retro_mputfur_257, retro_mputfur_33,
Mus musculus	ENSMUSG00000026021	5 retrocopies	retro_mmus_1594, retro_mmus_2129, retro_mmus_2135, retro_mmus_252, retro_mmus_2962,
Otolemur garnettii	ENSOGAG00000030345	1 retrocopy	retro_ogar_215,
Pongo abelii	ENSPPYG00000013083	3 retrocopies	retro_pabe_11, retro_pabe_1830, retro_pabe_775,
Pan troglodytes	ENSPTRG00000012817	1 retrocopy	retro_ptro_119,
Rattus norvegicus	ENSRNOG00000016133	2 retrocopies	retro_rnor_2015, retro_rnor_813,
Sarcophilus harrisii	ENSSHAG00000011968	1 retrocopy	retro_shar_375,
Ictidomys tridecemlineatus	ENSSTOG00000025405	4 retrocopies	retro_itri_1193, retro_itri_1232, retro_itri_216, retro_itri_668,
Tursiops truncatus	ENSTTRG00000000642	4 retrocopies	retro_ttru_1646, retro_ttru_1652, retro_ttru_309, retro_ttru_399,

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	0.04 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.03 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	0.00 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	0.00 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	0.03 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	0.00 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).