RetrogeneDB ID: retro_cjac_1

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:74614007..74615000(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022130
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: WDR5
• Ensembl ID: ENSCJAG00000010123
• Aliases: None
• Description: WD repeat domain 5 [Source:HGNC Symbol;Acc:12757]

Sequence

>retro_cjac_1
ATGGCAACGAAGGAGTCAGGAGATGCCCAAGCACAGTTGGCCCCCTCCTCATCTGCCAGTCAGAGCAAGGAAGTGCCTGA
AAACCCAAACTATGCTCTCAAATGTACTCTCGTGGGGCACACGGAAGCAGTATCATCAGTTAAGTTTAGTCCTAATGGAG
AATGGCTAGCAAGTTCTTCTGCTGATAGGCTAATCATAATTTGGGGAGCATATGATGGAAAATACGAGAAAACACTCTAT
GGTCATAATCTGGAAATATCGGATGTTGCCTGGTCATCAGATTCCAGTCGTCTTGTTTCTGCCTCAGATGATAAAACTCT
AAAGTTATGGGATGCGAGATCTGGAAAATGTTTGAAAACACTGGAGGGGCACAGTAATTATGTCTTTTGTTGTAACTTCA
ATCCGCCATCCAACCTTATCATCTCAGGATCTTTTGATGAGACTGTAAAAATATGGGAGGTAAAAACGGGAAACTGCCTC
AAGACTTTATCTGCTCATTCTGACCCAGTTTCTGCTGTTCATTTTAATTGTAGTGGGTCCTTGATAGTGTCAGGTAGCTA
TGATGGCCTCTGTAGAATCTGGGATGCTGCATCAGGCCAGTGTTTAAAAACGCTCGTTGATGACGGTAACCCTCCTGTCT
CTTTTGTAAAATTTTCTCCAAATGGTAAATATATTCTCACTGCAACTTTGGACAATACTCTTAAACTATGGGATTATACC
AGAGGCAGATGCCTGAAAACATACACTGGTCATAAGAATGAGAAATATTGCATATTTGCCAATTTTTCAGTTACTGGTGG
AAAGTGGATTGTGTCTGGTTCTGAGGATAACCTGGTTTACATTTGGAACCTTCAGACCAAAGAGATTGTACAGAAATTAC
AAGGCCATACAGATGTCGTGATCTCAGCAGCTTGTCATCCTACAGAAAACCTCATTGCATCAGCAGCATTAGAAAATGAC
AAAACAATTAAACTGTGGATGAGTAACCACTAA

Alignment

ORF - retro_cjac_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.23 %
• 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..PSSSA.QSK..P..PNYALK.TL.GHT.AVSSVKFSPNGEWLASSSAD.LI.IWGAYDGK
Retrocopy ESGDAQAQLAPSSSASQSKEVPENPNYALKCTLVGHTEAVSSVKFSPNGEWLASSSADRLIIIWGAYDGK

Parental  FEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGS
          .EKT..GH.L.ISDVAWSSDS..LVSASDDKTLK.WD..SGKCLKTL.GHSNYVFCCNFNP.SNLI.SGS
Retrocopy YEKTLYGHNLEISDVAWSSDSSRLVSASDDKTLKLWDARSGKCLKTLEGHSNYVFCCNFNPPSNLIISGS

Parental  FDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVS
          FDE.V.IW.VKTG.CLKTL.AHSDPVSAVHFN..GSLIVS.SYDGLCRIWD.ASGQCLKTL.DD.NPPVS
Retrocopy FDETVKIWEVKTGNCLKTLSAHSDPVSAVHFNCSGSLIVSGSYDGLCRIWDAASGQCLKTLVDDGNPPVS

Parental  FVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL
          FVKFSPNGKYIL.ATLDNTLKLWDY..G.CLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL
Retrocopy FVKFSPNGKYILTATLDNTLKLWDYTRGRCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL

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
SRP051959_colon	3.55 RPM	5.86 RPM
SRP051959_heart	1.37 RPM	11.09 RPM
SRP051959_kidney	3.04 RPM	10.85 RPM
SRP051959_liver	2.51 RPM	6.80 RPM
SRP051959_lung	3.01 RPM	11.35 RPM
SRP051959_lymph_node	3.65 RPM	9.68 RPM
SRP051959_skeletal_muscle	1.05 RPM	9.37 RPM
SRP051959_spleen	3.78 RPM	10.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_11
Pan troglodytes	retro_ptro_18
Gorilla gorilla	retro_ggor_171
Macaca mulatta	retro_mmul_190
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 29 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	ENSCJAG00000005272	1 retrocopy	retro_cjac_3664,
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	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,
Nomascus leucogenys	ENSNLEG00000013472	1 retrocopy	retro_nleu_63,
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,