RetrogeneDB ID: retro_hsap_3502

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:100978151..100978925(+)
• Located in intron of: ENSG00000112249

Retrocopy information

• Ensembl ID: ENSG00000220695
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DCUN1D1
• Ensembl ID: ENSG00000043093
• Aliases: None
• Description: DCN1, defective in cullin neddylation 1, domain containing 1 [Source:HGNC Symbol;Acc:18184]

Sequence

>retro_hsap_3502
ATGAACAAGTTGAAATCATCGCAGAAGGATAAAGTTTGTCAGTTTATGATCTTCACACAATCTAGTGAAAAAAACCGCAG
TAAGTTGTCTATCTCAAAATGACTGGAAGTTAGATGTTGCAACAGATAATTTTTTCCAAAATCCTGAACTTTATATATGA
GAGAGTGTAAAAGGATCACTGGAAAGGAAGAAGTTAGAACAACTGTACAATAGAGACAAAGATCCTCAAAATGAGAATAA
AATTGGAATAGATGGTATATAGCAGTTCTGTGATGGCCTGGCACTCAATCCAGCCAGCATTAGTGTGTTGATTATTGCAT
GGATGTTCAGAGCAGCAATACAGTGTGAGTTCTCCAAACAGGAGTTCATGGATGGCATGACAGAATTAGGATGTGACAGC
ATAGAAAAACTAAAGGCCCAGATACCCAAGATGTAACAAGAATTGAAAGAACCAGGACAATTTAAGGATTTTTACCAGTT
TACTTTTAATTTTGCAAAGAATCCAAGACAAAAAGGATTAGATCTAGAAATGGCCATTGCCTACTGGAACTTAGTGCTTA
ATAGAAGATTTAAATTCTTAGACTTATGGAATAAATTTTTGTGGAACATCACAAACAATCAATACCAAAAGACACTTGGA
ATCTTCTTTTAGACTTCAGTACAGTGATTGCAAATCACGTGTCTAATTATGATGAAGGAGCATGGCCTGTTCTTATTGAT
GACTTTGTGGAATTTGCACGCCCTCAAACTGCTGGGACAAAAAGTACAACAGTG

Alignment

ORF - retro_hsap_3502 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNKLKSSQKDKVRQFMIFTQSSEK-TAVSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLY
          MNKLKSSQKDKV.QFMIFTQSSEK.TAVSCLSQNDWKLDVATDNFFQNPELYI.ESVKGSL.RKKLEQLY
Retrocopy MNKLKSSQKDKVCQFMIFTQSSEK>TAVSCLSQNDWKLDVATDNFFQNPELYI*ESVKGSLERKKLEQLY

Parental  NRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKA
          NR.KDPQ.ENKIGIDGI.QFCD.LAL.PASISVLIIAW.FRAA.QCEFSKQEFMDGMTELGCDSIEKLKA
Retrocopy NRDKDPQNENKIGIDGI*QFCDGLALNPASISVLIIAWMFRAAIQCEFSKQEFMDGMTELGCDSIEKLKA

Parental  QIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFL-LEHHKRSI
          QIPKM.QELKEPG.FKDFYQFTFNFAKNP.QKGLDLEMAIAYWNLVLN.RFKFLDLWNKFL..EHHK.SI
Retrocopy QIPKM*QELKEPGQFKDFYQFTFNFAKNPRQKGLDLEMAIAYWNLVLNRRFKFLDLWNKFL<VEHHKQSI

Parental  PKDTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV
          PKDTWNLLLDFST.IA...SNYD.EGAWPVLIDDFVEFARPQ.AGTKSTTV
Retrocopy PKDTWNLLLDFSTVIANHVSNYD-EGAWPVLIDDFVEFARPQTAGTKSTTV

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	37.25 RPM
bodymap2_adrenal	0.04 RPM	33.55 RPM
bodymap2_brain	0.00 RPM	59.30 RPM
bodymap2_breast	0.04 RPM	61.50 RPM
bodymap2_colon	0.00 RPM	38.17 RPM
bodymap2_heart	0.09 RPM	31.49 RPM
bodymap2_kidney	0.00 RPM	55.94 RPM
bodymap2_liver	0.02 RPM	35.28 RPM
bodymap2_lung	0.00 RPM	31.28 RPM
bodymap2_lymph_node	0.00 RPM	37.70 RPM
bodymap2_ovary	0.00 RPM	55.04 RPM
bodymap2_prostate	0.00 RPM	54.80 RPM
bodymap2_skeletal_muscle	0.00 RPM	51.44 RPM
bodymap2_testis	0.02 RPM	150.05 RPM
bodymap2_thyroid	0.00 RPM	53.10 RPM
bodymap2_white_blood_cells	0.00 RPM	65.28 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3502 was not detected

EST

No EST(s) were mapped for retro_hsap_3502 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_157155	115 libraries	26 libraries	444 libraries	700 libraries	544 libraries

The graphical summary, for retro_hsap_3502 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_3502 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3502 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2374
Gorilla gorilla	retro_ggor_2368
Pongo abelii	retro_pabe_2894
Macaca mulatta	retro_mmul_1782

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013358	14 retrocopies	retro_chof_1054, retro_chof_1129, retro_chof_1198, retro_chof_1373, retro_chof_1546, retro_chof_1728, retro_chof_2049, retro_chof_232, retro_chof_2329, retro_chof_2369, retro_chof_2373, retro_chof_479, retro_chof_767, retro_chof_812,
Callithrix jacchus	ENSCJAG00000005148	2 retrocopies	retro_cjac_1423, retro_cjac_2358,
Cavia porcellus	ENSCPOG00000022086	4 retrocopies	retro_cpor_1289, retro_cpor_756, retro_cpor_758, retro_cpor_870,
Dasypus novemcinctus	ENSDNOG00000019073	2 retrocopies	retro_dnov_1494, retro_dnov_840,
Echinops telfairi	ENSETEG00000000166	1 retrocopy	retro_etel_1460,
Homo sapiens	ENSG00000043093	1 retrocopy	retro_hsap_3502 ,
Gorilla gorilla	ENSGGOG00000010767	1 retrocopy	retro_ggor_2368,
Macaca mulatta	ENSMMUG00000010552	1 retrocopy	retro_mmul_1782,
Mustela putorius furo	ENSMPUG00000002369	1 retrocopy	retro_mputfur_919,
Mus musculus	ENSMUSG00000027708	1 retrocopy	retro_mmus_1009,
Nomascus leucogenys	ENSNLEG00000005983	1 retrocopy	retro_nleu_793,
Otolemur garnettii	ENSOGAG00000000658	1 retrocopy	retro_ogar_3499,
Pan troglodytes	ENSPTRG00000015661	1 retrocopy	retro_ptro_2374,
Tarsius syrichta	ENSTSYG00000012276	1 retrocopy	retro_tsyr_669,