RetrogeneDB ID: retro_hsap_11

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:122133382..122134375(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000196981
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: WDR5
• Ensembl ID: ENSG00000196363
• Aliases: WDR5, BIG-3, SWD3
• Description: WD repeat domain 5 [Source:HGNC Symbol;Acc:12757]

Sequence

>retro_hsap_11
ATGGCAACCAAGGAGTCAAGAGACGCCAAAGCACAGTTGGCCCTCTCCTCATCGGCCAATCAGAGCAAGGAAGTGCCTGA
AAACCCAAACTATGCTCTCAAATGTACTCTTGTGGGACACACGGAAGCAGTGTCATCAGTTAAGTTTAGTCCTAATGGAG
AATGGCTAGCAAGTTCTTCTGCTGATAGGCTAATCATAATTTGGGGAGCATATGATGGAAAATATGAGAAAACACTCTAT
GGTCATAATTTGGAAATATCGGATGTTGCCTGGTCATCAGATTCCAGTCGTCTTGTTTCTGCCTCAGATGATAAAACTCT
AAAATTATGGGATGTGAGATCTGGAAAATGTTTGAAAACACTGAAGGGGCACAGTAATTATGTCTTTTGTTGTAACTTCA
ATCCGCCATCCAACCTTATAATCTCGGGATCTTTTGATGAGACTGTAAAAATATGGGAGGTGAAAACAGGAAAGTGTCTC
AAGACTTTGTCTGCTCATTCTGACCCAGTTTCTGCTGTTCATTTTAATTGTAGTGGGTCCTTGATAGTGTCAGGTAGCTA
TGATGGCCTCTGTAGAATCTGGGATGCTGCATCAGGTCAGTGTTTAAAAACGCTCGTTGATGACGATAACCCTCCTGTCT
CTTTTGTAAAATTTTCTCCAAATGGTAAATACATTCTCACTGCAACTTTGGACAACACTCTTAAACTATGGGATTATAGC
AGAGGCAGGTGCCTGAAAACATACACTGGTCATAAGAATGAGAAATATTGCATATTTGCCAATTTTTCAGTTACTGGTGG
AAAGTGGATTGTGTCTGGTTCCGAGGATAACCTGGTTTACATTTGGAACCTTCAGACTAAAGAGATTGTGCAGAAATTAC
AAGGCCATACAGATGTTGTGATCTCAGCAGCTTGTCATCCTACAGAAAACCTCATCGCATCAGCAGCATTAGAAAATGAC
AAAACAATTAAACTGTGGATGAGTAACCACTAA

Alignment

ORF - retro_hsap_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.46 %
• Parental protein coverage: 97.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETEAARAQPTPSSSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGK
          E...A.AQ...SSSA.QSK..P..PNYALK.TL.GHT.AVSSVKFSPNGEWLASSSAD.LI.IWGAYDGK
Retrocopy ESRDAKAQLALSSSANQSKEVPENPNYALKCTLVGHTEAVSSVKFSPNGEWLASSSADRLIIIWGAYDGK

Parental  FEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGS
          .EKT..GH.L.ISDVAWSSDS..LVSASDDKTLK.WDV.SGKCLKTLKGHSNYVFCCNFNP.SNLI.SGS
Retrocopy YEKTLYGHNLEISDVAWSSDSSRLVSASDDKTLKLWDVRSGKCLKTLKGHSNYVFCCNFNPPSNLIISGS

Parental  FDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVS
          FDE.V.IW.VKTGKCLKTL.AHSDPVSAVHFN..GSLIVS.SYDGLCRIWD.ASGQCLKTL.DDDNPPVS
Retrocopy FDETVKIWEVKTGKCLKTLSAHSDPVSAVHFNCSGSLIVSGSYDGLCRIWDAASGQCLKTLVDDDNPPVS

Parental  FVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL
          FVKFSPNGKYIL.ATLDNTLKLWDYS.G.CLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL
Retrocopy FVKFSPNGKYILTATLDNTLKLWDYSRGRCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL

Parental  QTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSD
          QTKEIVQKLQGHTDVVIS.ACHPTEN.IASAALENDKTIKLW.S.
Retrocopy QTKEIVQKLQGHTDVVISAACHPTENLIASAALENDKTIKLWMSN

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	2.05 RPM	18.61 RPM
bodymap2_adrenal	3.50 RPM	23.56 RPM
bodymap2_brain	1.20 RPM	16.71 RPM
bodymap2_breast	4.46 RPM	21.56 RPM
bodymap2_colon	1.70 RPM	24.36 RPM
bodymap2_heart	1.85 RPM	15.08 RPM
bodymap2_kidney	5.01 RPM	26.53 RPM
bodymap2_liver	1.41 RPM	18.42 RPM
bodymap2_lung	1.95 RPM	11.76 RPM
bodymap2_lymph_node	3.53 RPM	26.64 RPM
bodymap2_ovary	10.72 RPM	40.33 RPM
bodymap2_prostate	3.46 RPM	23.17 RPM
bodymap2_skeletal_muscle	1.36 RPM	53.02 RPM
bodymap2_testis	5.94 RPM	82.29 RPM
bodymap2_thyroid	9.15 RPM	33.90 RPM
bodymap2_white_blood_cells	6.24 RPM	26.54 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_11 in 53 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001VKU	POLR2A	3:122134727..122135393
ENCFF002CFW	POLR2A	3:122134724..122135446
ENCFF002CFX	POLR2A	3:122134736..122135449
ENCFF002CGN	POLR2A	3:122134709..122135407
ENCFF002CHO	POLR2A	3:122134582..122135550
ENCFF002CIH	POLR2A	3:122134942..122135410
ENCFF002CIO	POLR2A	3:122134676..122135440
ENCFF002CJE	POLR2A	3:122134877..122135464
ENCFF002CJZ	POLR2A	3:122134691..122135516
ENCFF002CKX	POLR2A	3:122134710..122135424
ENCFF002CLM	POLR2A	3:122134848..122135388
ENCFF002CMI	POLR2A	3:122134672..122135516
ENCFF002COJ	POLR2A	3:122134811..122135247
ENCFF002COJ	POLR2A	3:122135028..122135464
ENCFF002CPG	POLR2A	3:122134946..122135378
ENCFF002CPH	POLR2A	3:122134919..122135309
ENCFF002CQA	POLR2A	3:122134908..122135427
ENCFF002CQC	POLR2A	3:122134736..122135426
ENCFF002CQE	POLR2A	3:122134977..122135427
ENCFF002CQG	POLR2A	3:122134973..122135416
ENCFF002CQI	POLR2A	3:122134946..122135403
ENCFF002CQK	POLR2A	3:122134692..122135433
ENCFF002CQM	POLR2A	3:122134921..122135417
ENCFF002CQO	POLR2A	3:122134681..122135454
ENCFF002CRK	POLR2A	3:122134884..122135408
ENCFF002CRK	POLR2A	3:122135084..122135608
ENCFF002CRO	POLR2A	3:122135082..122135220
ENCFF002CSY	POLR2A	3:122134646..122135528
ENCFF002CUP	POLR2A	3:122135061..122135140
ENCFF002CUQ	POLR2A	3:122134736..122135353
ENCFF002CVF	POLR2A	3:122135028..122135219
ENCFF002CVJ	POLR2A	3:122134791..122135339
ENCFF002CXM	POLR2A	3:122134995..122135245
ENCFF002CXN	POLR2A	3:122135017..122135273
ENCFF002CXO	POLR2A	3:122135009..122135255
ENCFF002CXP	POLR2A	3:122134922..122135326
ENCFF002CXQ	POLR2A	3:122135062..122135712
ENCFF002CXR	POLR2A	3:122134985..122135266
ENCFF002CZC	POLR2A	3:122134653..122135584
ENCFF002CZD	POLR2A	3:122134684..122135465
ENCFF002CZQ	POLR2A	3:122134760..122135283
ENCFF002CZW	POLR2A	3:122134549..122135499
ENCFF002CZY	POLR2A	3:122134690..122135462
ENCFF002DAE	POLR2A	3:122134972..122135282
ENCFF002DAE	POLR2A	3:122134743..122135053
ENCFF002DAH	POLR2A	3:122134984..122135268
ENCFF002DAK	POLR2A	3:122135028..122135177
ENCFF002DAS	POLR2A	3:122134874..122135350
ENCFF002DAV	POLR2A	3:122134990..122135276
ENCFF002DAY	POLR2A	3:122134997..122135321
ENCFF002DBB	POLR2A	3:122135055..122135255
ENCFF002DBB	POLR2A	3:122134787..122134987
ENCFF002DBE	POLR2A	3:122134736..122135035
ENCFF002DBE	POLR2A	3:122134924..122135206
ENCFF002DBO	POLR2A	3:122134785..122135169
ENCFF002DBP	POLR2A	3:122134824..122135016
ENCFF002DBP	POLR2A	3:122134966..122135156
ENCFF002DBP	POLR2A	3:122135222..122135386
ENCFF002DBQ	POLR2A	3:122135011..122135267
ENCFF002DBT	POLR2A	3:122135102..122135194

EST

4 EST(s) were mapped to retro_hsap_11 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AV657168	122133548	122133931	99.7	328	1	326
AW627765	122133329	122133760	99.8	429	1	428
BQ372613	122133685	122134053	99.5	365	2	362
R83779	122133386	122133794	95.5	394	1	382

TSS

No TSS is located nearby retro_hsap_11 retrocopy 5' end.

Lab

retro_hsap_11 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_11 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_18
Gorilla gorilla	retro_ggor_171
Macaca mulatta	retro_mmul_190
Callithrix jacchus	retro_cjac_1
Mus musculus	retro_mmus_132
Rattus norvegicus	retro_rnor_258
Bos taurus	retro_btau_299
Sus scrofa	retro_sscr_1
Canis familiaris	retro_cfam_128
Equus caballus	retro_ecab_82

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011179	1 retrocopy	retro_amel_29,
Bos taurus	ENSBTAG00000047031	1 retrocopy	retro_btau_299,
Canis familiaris	ENSCAFG00000019830	1 retrocopy	retro_cfam_128,
Callithrix jacchus	ENSCJAG00000010123	1 retrocopy	retro_cjac_1,
Cavia porcellus	ENSCPOG00000014790	1 retrocopy	retro_cpor_12,
Dipodomys ordii	ENSDORG00000015010	1 retrocopy	retro_dord_7,
Equus caballus	ENSECAG00000017389	1 retrocopy	retro_ecab_82,
Echinops telfairi	ENSETEG00000015731	1 retrocopy	retro_etel_15,
Felis catus	ENSFCAG00000005712	1 retrocopy	retro_fcat_119,
Homo sapiens	ENSG00000007168	2 retrocopies	retro_hsap_2144, retro_hsap_2292,
Homo sapiens	ENSG00000122692	1 retrocopy	retro_hsap_457,
Homo sapiens	ENSG00000196363	1 retrocopy	retro_hsap_11 ,
Gorilla gorilla	ENSGGOG00000004997	2 retrocopies	retro_ggor_171, retro_ggor_2023,
Loxodonta africana	ENSLAFG00000011192	1 retrocopy	retro_lafr_55,
Microcebus murinus	ENSMICG00000008085	1 retrocopy	retro_mmur_34,
Myotis lucifugus	ENSMLUG00000002236	1 retrocopy	retro_mluc_11,
Macaca mulatta	ENSMMUG00000014159	1 retrocopy	retro_mmul_190,
Mustela putorius furo	ENSMPUG00000012184	1 retrocopy	retro_mputfur_2,
Mus musculus	ENSMUSG00000026917	1 retrocopy	retro_mmus_132,
Otolemur garnettii	ENSOGAG00000008960	1 retrocopy	retro_ogar_86,
Procavia capensis	ENSPCAG00000013476	1 retrocopy	retro_pcap_43,
Pan troglodytes	ENSPTRG00000023653	2 retrocopies	retro_ptro_18, retro_ptro_1975,
Pteropus vampyrus	ENSPVAG00000001666	1 retrocopy	retro_pvam_112,
Rattus norvegicus	ENSRNOG00000008212	1 retrocopy	retro_rnor_258,
Sus scrofa	ENSSSCG00000024912	1 retrocopy	retro_sscr_1,
Ictidomys tridecemlineatus	ENSSTOG00000015899	1 retrocopy	retro_itri_117,
Drosophila melanogaster	FBgn0040066	1 retrocopy	retro_dmel_69,