RetrogeneDB ID: retro_hsap_1960

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 19:9885172..9885633(+)
• Located in intron of: ENSG00000196605

Retrocopy information

• Ensembl ID: ENSG00000267741
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2L3
• Ensembl ID: ENSG00000185651
• Aliases: UBE2L3, E2-F1, L-UBC, UBCH7, UbcM4
• Description: ubiquitin-conjugating enzyme E2L 3 [Source:HGNC Symbol;Acc:12488]

Sequence

>retro_hsap_1960
ATGGCGGCCAGCAGGAGGCTGATTAAGAGCTTGAGGAAATCTGCAAATGTGGGATGAAAAACTTCCCGTAACATCCAGGT
TGATGAAGCTAATTTATTGACTTAGCAAGGGCTTATTGTTCCTGACAACTCTCCATATGATTAGGTGACCTTCAGAATCG
AAATCAACTTTCCAGCAGAGTATCCATTCAAACTACCAAAGATCACATTTAAAACAAAGATCTATCACCCAAATATCGAC
GAAAAGGGGCAGGTCTGTCTGTCAGTAATTAGTGCTGAAAACTGGAAGCCAGCAACCAAAACCGACCAAGTAATCCAGTC
CCTCATAGCACTGGTGAATGACCCCCAGCCCGAGCACCCGCTTCGGGCTGACCTAGCTGAAGAATACTCTAAGGACCGTA
AAAAATTCTGTAAGAATGCTGAAGAGTTTACAAAGAAATATGGGGAAAGTGACCTGTGGAC

Alignment

ORF - retro_hsap_1960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAASRRLMK-ELEEIRKCGMKNF-RNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKI
          MAASRRL.K.ELEEI.KCGMKNF.RNIQVDEANLLT.QGLIVPDN.PYD...FRIEINFPAEYPFK.PKI
Retrocopy MAASRRLIK<ELEEICKCGMKNF>RNIQVDEANLLT*QGLIVPDNSPYD*VTFRIEINFPAEYPFKLPKI

Parental  TFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCK
          TFKTKIYHPNIDEKGQVCL.VISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCK
Retrocopy TFKTKIYHPNIDEKGQVCLSVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCK

Parental  NAEEFTKKYGE-KRPVD
          NAEEFTKKYGE.K.PVD
Retrocopy NAEEFTKKYGE<K*PVD

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	0.14 RPM	64.74 RPM
bodymap2_adrenal	0.23 RPM	69.58 RPM
bodymap2_brain	0.02 RPM	65.09 RPM
bodymap2_breast	0.00 RPM	75.39 RPM
bodymap2_colon	0.00 RPM	66.79 RPM
bodymap2_heart	0.07 RPM	56.79 RPM
bodymap2_kidney	0.00 RPM	66.32 RPM
bodymap2_liver	0.06 RPM	42.97 RPM
bodymap2_lung	0.00 RPM	60.13 RPM
bodymap2_lymph_node	0.09 RPM	81.52 RPM
bodymap2_ovary	0.17 RPM	69.49 RPM
bodymap2_prostate	0.00 RPM	79.95 RPM
bodymap2_skeletal_muscle	0.00 RPM	66.00 RPM
bodymap2_testis	0.02 RPM	74.30 RPM
bodymap2_thyroid	0.08 RPM	65.87 RPM
bodymap2_white_blood_cells	0.00 RPM	108.36 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1960 was not detected

EST

No EST(s) were mapped for retro_hsap_1960 retrocopy.

TSS

No TSS is located nearby retro_hsap_1960 retrocopy 5' end.

Lab

retro_hsap_1960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1960 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000019274	1 retrocopy	retro_ecab_116,
Homo sapiens	ENSG00000072401	2 retrocopies	retro_hsap_4723, retro_hsap_4725,
Homo sapiens	ENSG00000078967	2 retrocopies	retro_hsap_452, retro_hsap_453,
Homo sapiens	ENSG00000170035	1 retrocopy	retro_hsap_4653,
Homo sapiens	ENSG00000185651	4 retrocopies	retro_hsap_1094, retro_hsap_1185, retro_hsap_1338, retro_hsap_1960 ,
Myotis lucifugus	ENSMLUG00000001547	1 retrocopy	retro_mluc_32,
Nomascus leucogenys	ENSNLEG00000000192	1 retrocopy	retro_nleu_97,
Oryctolagus cuniculus	ENSOCUG00000002610	3 retrocopies	retro_ocun_826, retro_ocun_932, retro_ocun_937,
Pongo abelii	ENSPPYG00000011602	1 retrocopy	retro_pabe_99,
Pan troglodytes	ENSPTRG00000014114	1 retrocopy	retro_ptro_123,
Pteropus vampyrus	ENSPVAG00000013575	1 retrocopy	retro_pvam_727,
Sorex araneus	ENSSARG00000005137	3 retrocopies	retro_sara_105, retro_sara_277, retro_sara_653,
Ictidomys tridecemlineatus	ENSSTOG00000016293	2 retrocopies	retro_itri_1528, retro_itri_655,
Tetraodon nigroviridis	ENSTNIG00000010600	1 retrocopy	retro_tnig_16,
Takifugu rubripes	ENSTRUG00000003392	1 retrocopy	retro_trub_39,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.12 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.13 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.05 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.02 RPM

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Indel association:

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