RetrogeneDB ID: retro_cjac_1101

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:56697432..56698248(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ATAD1
• Ensembl ID: ENSCJAG00000005296
• Aliases: None
• Description: None

Sequence

>retro_cjac_1101
ATGCATGTTACTTGGAGTGATATAACAGGTTTTAGATGATGTCATTATGATCTGAAAAACACAGTCATCTTTCCTATCAA
AAAGAAACATTTGTTTGAGAATTCCAGGCTTCTGCAGCCTCCAAAAGTTGTACTTCTCTATTGGCCTCTAGGCTGTGGTA
AAACATTGATTGCCAAGACCACAGCCAAAGAAGCAGACTGTCGATTTATTAACCTTCAACCTCTGACCTATAAGTGATAT
GGAGAATCTCAAAAACTGGCTGCTGCTGTCTTCTCCCTTGCCATAAAACTACAACCATCCATCATCTTTATAGATGAAAT
AGACTCCTTTCTACAAAACCATTCAAGTTATGACCACGAAGCTACAGCCATGATGAAAGCTCAGTTTTTTGAGTCTCTGG
GATGGATTACATATTGATCATAGCTGCCAGGTCATAGTAATGGGAGCTACCCATCGTCCTCAGAACCTTGACTAGGCTAT
AAGGAAAAGAATGCCTACAATATTTTATATCAACCAGCCTGCTTTAAAACAGAGAGAAGCAATCCTGAAGCTCATCTTGA
AAAATGAAAATGTGGACAGACATGTAGAAAAATGCTAGAAGTTGCCCAGGAAACTGATGGGTTTTCAGGAAGTGACCTAA
AAGAGATGTGTCAAGATGTTGCCCTCCTCTGTGTTAGAGAATATGTTAATTCTAGGTCAGAAGAAAGCCATGACGAAGAT
TAAATTTGGCCTGTTTAACAGGAACACCTACATCAGGCAACTGAAAAGATGATGAAATCAAAGGATGCAGCATTTCAGAA
TGTTTTAACACATTTG

Alignment

ORF - retro_cjac_1101 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.58 %
• Parental protein coverage: 98.91 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MHVTWSDIAG-LDDVIT-DLKDTVILPIKKKHLFENSRLLQPPKGVLLYGPPGCGKTLIAKATAKEAGCR
          MHVTWSDI.G.LDDVI..DLK.TVI.PIKKKHLFENSRLLQPPK.VLLY.P.GCGKTLIAK.TAKEA.CR
Retrocopy MHVTWSDITG>LDDVIM<DLKNTVIFPIKKKHLFENSRLLQPPKVVLLYWPLGCGKTLIAKTTAKEADCR

Parental  FINLQPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLRNRSSSDHEATAMMKAQ-FMSLWDG
          FINLQP..LT.K.YGESQKLAAAVFSLAIKLQPSIIFIDEIDSFL.N.SS.DHEATAMMKAQ.F.SLWDG
Retrocopy FINLQP--LTYK*YGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLQNHSSYDHEATAMMKAQ>FLSLWDG

Parental  LDTDHSCQVIVMGATNRPQDLDSAIMRRMPTRFHINQPALKQREAILKLILKNENVDRHVDLL-EVAQET
          L..DHSCQVIVMGAT.RPQ.LD.AI..RMPT.F.INQPALKQREAILKLILKNENVDRHV..........
Retrocopy LHIDHSCQVIVMGATHRPQNLD*AIRKRMPTIFYINQPALKQREAILKLILKNENVDRHVEKC*KLPRKL

Parental  DGF-SGSDLKEMCRDAALLCVREYVNSTAEESHDEDEIRPVQQQDLHRAIEKMKKSKDAAFQNVLTHV
          .GF.SGSDLKEMC.D.ALLCVREYVNS..EESHDED.I.PV.Q..LH.A.EKM.KSKDAAFQNVLTH.
Retrocopy MGF<SGSDLKEMCQDVALLCVREYVNSRSEESHDED*IWPV*QEHLHQATEKMMKSKDAAFQNVLTHL

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	0.00 RPM	20.68 RPM
SRP051959_heart	0.00 RPM	23.12 RPM
SRP051959_kidney	0.00 RPM	25.07 RPM
SRP051959_liver	0.00 RPM	13.73 RPM
SRP051959_lung	0.00 RPM	22.34 RPM
SRP051959_lymph_node	0.00 RPM	18.95 RPM
SRP051959_skeletal_muscle	0.00 RPM	24.92 RPM
SRP051959_spleen	0.00 RPM	17.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1101 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1101 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1101 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1900
Pan troglodytes	retro_ptro_1255
Gorilla gorilla	retro_ggor_1393

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005296	1 retrocopy	retro_cjac_1101 ,
Homo sapiens	ENSG00000138138	1 retrocopy	retro_hsap_1900,
Gorilla gorilla	ENSGGOG00000026651	1 retrocopy	retro_ggor_1393,
Macaca mulatta	ENSMMUG00000006414	1 retrocopy	retro_mmul_608,
Nomascus leucogenys	ENSNLEG00000012135	1 retrocopy	retro_nleu_1231,
Oryctolagus cuniculus	ENSOCUG00000012082	1 retrocopy	retro_ocun_1634,
Pan troglodytes	ENSPTRG00000002717	1 retrocopy	retro_ptro_1255,
Pteropus vampyrus	ENSPVAG00000014020	1 retrocopy	retro_pvam_1080,
Rattus norvegicus	ENSRNOG00000010861	1 retrocopy	retro_rnor_2752,
Ictidomys tridecemlineatus	ENSSTOG00000006563	1 retrocopy	retro_itri_309,