RetrogeneDB ID: retro_hsap_75

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 18:11851510..11852110(+)
• Located in intron of: ENSG00000141404

Retrocopy information

• Ensembl ID: ENSG00000255112
• Aliases: CHMP1B, C10orf2, C18-ORF2, C18orf2, CHMP1.5, Vps46-2, Vps46B, hVps46-2
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CHMP1A
• Ensembl ID: ENSG00000131165
• Aliases: CHMP1A, CHMP1, PCH8, PCOLN3, PRSM1, VPS46-1, VPS46A
• Description: charged multivesicular body protein 1A [Source:HGNC Symbol;Acc:8740]

Sequence

>retro_hsap_75
ATGTCTAACATGGAGAAACACCTGTTCAACCTGAAGTTCGCGGCCAAAGAACTGAGTAGGAGTGCCAAAAAATGCGATAA
GGAGGAAAAGGCCGAAAAGGCCAAAATTAAAAAGGCCATTCAGAAGGGCAACATGGAAGTTGCGAGGATACACGCCGAAA
ATGCCATCCGCCAGAAGAACCAGGCGGTGAATTTCTTGAGAATGAGTGCGCGAGTCGATGCAGTGGCTGCCAGGGTCCAG
ACGGCGGTGACGATGGGCAAGGTGACCAAGTCGATGGCTGGTGTGGTTAAGTCGATGGATGCGACATTGAAGACCATGAA
TCTGGAGAAGATTTCTGCTTTGATGGACAAATTCGAGCACCAGTTTGAGACTCTGGACGTCCAGACGCAGCAAATGGAAG
ACACGATGAGCAGCACGACGACGCTCACCACTCCCCAGAACCAAGTGGATATGCTGCTCCAGGAAATGGCAGATGAGGCG
GGCCTCGACCTCAACATGGAGCTGCCGCAGGGCCAGACCGGCTCCGTGGGCACGAGCGTGGCTTCGGCGGAGCAGGATGA
ACTGTCTCAGAGACTGGCCCGCCTTCGGGATCAAGTGTGA

Alignment

ORF - retro_hsap_75 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDDTLFQLKFTAKQLEKLAKKAEKDSKAEQAKVKKALLQKNVECARVYAENAIRKKNEGVNWLRMASRVD
          M...LF.LKF.AK.L...AKK..K..KAE.AK.KKA....N.E.AR..AENAIR.KN..VN.LRM..RVD
Retrocopy MEKHLFNLKFAAKELSRSAKKCDKEEKAEKAKIKKAIQKGNMEVARIHAENAIRQKNQAVNFLRMSARVD

Parental  AVASKVQTAVTMKGVTKNMAQVTKALDKALSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDSMSSATTLT
          AVA..VQTAVTM..VTK.MA.V.K..D..L.TM.L.K.S..MD.FE.Q...LDV.T..MED.MSS.TTLT
Retrocopy AVAARVQTAVTMGKVTKSMAGVVKSMDATLKTMNLEKISALMDKFEHQFETLDVQTQQMEDTMSSTTTLT

Parental  TPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVRSQEDQLSRRLAALRN
          TPQ.QVD.L....A.E.GL.....L.Q...G...VG.S......D.LS.RLA.LR.
Retrocopy TPQNQVDMLLQEMADEAGLDLNMELPQGQTG--SVGTSVASAEQDELSQRLARLRD

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	19.96 RPM	43.71 RPM
bodymap2_adrenal	15.58 RPM	44.56 RPM
bodymap2_brain	12.61 RPM	19.27 RPM
bodymap2_breast	14.55 RPM	38.68 RPM
bodymap2_colon	10.33 RPM	32.64 RPM
bodymap2_heart	14.01 RPM	14.93 RPM
bodymap2_kidney	16.40 RPM	39.50 RPM
bodymap2_liver	6.00 RPM	16.43 RPM
bodymap2_lung	21.92 RPM	31.45 RPM
bodymap2_lymph_node	19.86 RPM	34.85 RPM
bodymap2_ovary	10.60 RPM	46.77 RPM
bodymap2_prostate	24.49 RPM	43.79 RPM
bodymap2_skeletal_muscle	174.42 RPM	32.25 RPM
bodymap2_testis	12.67 RPM	47.21 RPM
bodymap2_thyroid	64.69 RPM	46.76 RPM
bodymap2_white_blood_cells	36.30 RPM	60.30 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_75 in 52 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001VKU	POLR2A	18:11851077..11851777
ENCFF002CFW	POLR2A	18:11851099..11851621
ENCFF002CFX	POLR2A	18:11851107..11851591
ENCFF002CGN	POLR2A	18:11851124..11851479
ENCFF002CHO	POLR2A	18:11851045..11851674
ENCFF002CIH	POLR2A	18:11851328..11851583
ENCFF002CIO	POLR2A	18:11851111..11851616
ENCFF002CJE	POLR2A	18:11851049..11851671
ENCFF002CJZ	POLR2A	18:11850833..11851665
ENCFF002CKX	POLR2A	18:11851090..11851577
ENCFF002CLM	POLR2A	18:11851129..11851312
ENCFF002CMI	POLR2A	18:11851058..11851656
ENCFF002COJ	POLR2A	18:11851045..11851481
ENCFF002CPG	POLR2A	18:11851122..11851379
ENCFF002CPG	POLR2A	18:11851385..11851540
ENCFF002CPH	POLR2A	18:11851058..11851448
ENCFF002CQA	POLR2A	18:11851059..11851421
ENCFF002CQA	POLR2A	18:11851171..11851741
ENCFF002CQC	POLR2A	18:11851104..11851574
ENCFF002CQE	POLR2A	18:11851087..11851588
ENCFF002CQG	POLR2A	18:11851124..11851432
ENCFF002CQG	POLR2A	18:11851349..11851561
ENCFF002CQI	POLR2A	18:11851098..11851570
ENCFF002CQK	POLR2A	18:11851066..11851591
ENCFF002CQM	POLR2A	18:11851106..11851606
ENCFF002CQO	POLR2A	18:11851088..11851615
ENCFF002CRK	POLR2A	18:11850979..11851503
ENCFF002CRO	POLR2A	18:11851049..11851469
ENCFF002CSY	POLR2A	18:11850838..11852303
ENCFF002CUP	POLR2A	18:11851360..11851461
ENCFF002CUQ	POLR2A	18:11851109..11851421
ENCFF002CUQ	POLR2A	18:11851386..11851588
ENCFF002CUQ	POLR2A	18:11850015..11850519
ENCFF002CVF	POLR2A	18:11851324..11851617
ENCFF002CVJ	POLR2A	18:11850013..11852230
ENCFF002CXM	POLR2A	18:11851110..11851408
ENCFF002CXN	POLR2A	18:11851101..11851382
ENCFF002CXO	POLR2A	18:11851126..11851391
ENCFF002CXO	POLR2A	18:11851247..11851671
ENCFF002CXP	POLR2A	18:11851082..11851432
ENCFF002CXP	POLR2A	18:11851356..11851578
ENCFF002CXR	POLR2A	18:11851106..11851579
ENCFF002CZC	POLR2A	18:11850601..11852757
ENCFF002CZC	POLR2A	18:11850042..11850623
ENCFF002CZD	POLR2A	18:11850884..11851832
ENCFF002CZQ	POLR2A	18:11851105..11851492
ENCFF002CZQ	POLR2A	18:11851105..11851518
ENCFF002CZW	POLR2A	18:11850887..11851793
ENCFF002CZY	POLR2A	18:11851060..11851610
ENCFF002DAE	POLR2A	18:11851106..11851416
ENCFF002DAH	POLR2A	18:11851201..11851340
ENCFF002DAK	POLR2A	18:11851023..11851523
ENCFF002DAS	POLR2A	18:11851181..11851657
ENCFF002DAV	POLR2A	18:11851113..11851402
ENCFF002DAV	POLR2A	18:11851458..11851596
ENCFF002DAV	POLR2A	18:11850055..11850599
ENCFF002DAY	POLR2A	18:11851212..11851371
ENCFF002DBB	POLR2A	18:11851161..11851361
ENCFF002DBE	POLR2A	18:11851104..11851564
ENCFF002DBO	POLR2A	18:11851152..11851380
ENCFF002DBO	POLR2A	18:11851344..11851565
ENCFF002DBP	POLR2A	18:11851164..11851359
ENCFF002DBP	POLR2A	18:11851356..11851559
ENCFF002DBQ	POLR2A	18:11851165..11851333
ENCFF002DBT	POLR2A	18:11851069..11851439

EST

2 EST(s) were mapped to retro_hsap_75 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BG011449	11851582	11851729	98	144	3	141
R58238	11851491	11851811	99.7	316	1	312

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_65795	1586 libraries	173 libraries	50 libraries	14 libraries	6 libraries
TSS #2	TSS_65796	1622 libraries	148 libraries	39 libraries	12 libraries	8 libraries
TSS #3	TSS_65797	1594 libraries	161 libraries	46 libraries	15 libraries	13 libraries
TSS #4	TSS_65800	103 libraries	26 libraries	1094 libraries	528 libraries	78 libraries
TSS #5	TSS_65801	24 libraries	1 library	45 libraries	185 libraries	1574 libraries
TSS #6	TSS_65802	101 libraries	142 libraries	671 libraries	437 libraries	478 libraries
TSS #7	TSS_65803	1306 libraries	369 libraries	132 libraries	17 libraries	5 libraries

The graphical summary, for retro_hsap_75 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_75 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_75 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1278
Gorilla gorilla	retro_ggor_1368
Pongo abelii	retro_pabe_1581
Callithrix jacchus	retro_cjac_1147
Oryctolagus cuniculus	retro_ocun_1508
Rattus norvegicus	retro_rnor_1361
Canis familiaris	retro_cfam_1866
Equus caballus	retro_ecab_991

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001216	1 retrocopy	retro_amel_1749,
Bos taurus	ENSBTAG00000033331	1 retrocopy	retro_btau_1048,
Canis familiaris	ENSCAFG00000019822	1 retrocopy	retro_cfam_1866,
Callithrix jacchus	ENSCJAG00000010826	1 retrocopy	retro_cjac_1147,
Homo sapiens	ENSG00000131165	2 retrocopies	retro_hsap_359, retro_hsap_75 ,
Macaca mulatta	ENSMMUG00000014909	3 retrocopies	retro_mmul_1325, retro_mmul_476, retro_mmul_706,
Mustela putorius furo	ENSMPUG00000007281	1 retrocopy	retro_mputfur_383,
Mus musculus	ENSMUSG00000000743	1 retrocopy	retro_mmus_2260,
Oryctolagus cuniculus	ENSOCUG00000023371	1 retrocopy	retro_ocun_1508,
Otolemur garnettii	ENSOGAG00000004883	1 retrocopy	retro_ogar_170,
Pongo abelii	ENSPPYG00000007667	1 retrocopy	retro_pabe_344,
Pan troglodytes	ENSPTRG00000008483	2 retrocopies	retro_ptro_1278, retro_ptro_283,
Ictidomys tridecemlineatus	ENSSTOG00000023813	1 retrocopy	retro_itri_1311,