RetrogeneDB ID: retro_cjac_3982

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286469.1:236757..237699(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ESRRA
• Ensembl ID: ENSCJAG00000018030
• Aliases: None
• Description: estrogen-related receptor alpha [Source:HGNC Symbol;Acc:3471]

Sequence

>retro_cjac_3982
GGGAGCATCGAATACAGCTGTCTGGCTTTCAAAGAGTGTGAGATCATCAAGCAGAAACGCAAGGCCTGCCAGGCCTGCCA
CTTCACCAGGTGCTTGTGGGTGGGCATGCTCAAAAAGGGAGTGTACCTGGACTGCATCTGGGATGGGCAGCAGAAGTATA
AGTGGTGGCCATAGGTGGACACACTGCCCTTCCCAGGCCCCTTCCCTGCTGGGCCCCTGGCAGTAGCTGGAGGACCTCGG
AAGATAGCCCCAGTGAATGCACTGGTGTCTCATCTGCTTGTGGTTGAGCCTGAGAAGCTCTATGCCATGCCTGACCCCGC
AGGCTCTGATGCTCACCTCCCAGCCATGGCTACCCTCTGTCACCTCTTTCACTGAAAAATTGTGGTCACCATCAGCTGAA
CCAAGAGCATACCAGGGTTCTAATCGCTGTCGCTGTCGGACCAGATGTCAGTACTGTAGAGCATGTGGATGGAAGTGCTG
GTGCTGGGTGTGGCCCAGTGCTCACTGCCACAGCAGGATGAGCTGGCCTTTGCTGAGGACTTAGTCCTGGATGAAGAGGG
GACTCTGGCAGCTGGTCTGGGGGAACTGGGGGCTGGCCTGCTGCAGGTGGTTCAGTGACTGCAGGGTCTTCAGCTGGAGC
AAGAGGGGTACATACTCCTGAAGGCCCTGGCCTTTGCCAATTCAGGCTCTGTGCACATCAAAGATACCGAGGCTGTGGAA
AAGCTGTGAGAAGCCCTGCATGTGGCCCTGCTGGAGTACAAAGCCAGCCGGGCTGGCCCCAGAGGGGCTGCTGAGTGGCA
GCGGGAGGGCATGCTGCTGCTCACACTATTGCTCCTCCACCAGAGAGCAGGCAAAGTGCTGGCCCATCTCTTTGGGGTAA
AGCTGGAGAGCAAGGCGCCCATGCACAAGCTCTTCTTGGAGATGCTCAAGTCCATGATGGAT

Alignment

ORF - retro_cjac_3982 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.46 %
• Parental protein coverage: 74.47 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEVDPLPFPGPFPA
          GSIEYSC.A..ECEI.K..RKACQAC.FT.CL.VGMLK.GV.LD....G.QKYK..P.VD.LPFPGPFPA
Retrocopy GSIEYSCLAFKECEIIKQKRKACQACHFTRCLWVGMLKKGVYLDCIWDGQQKYKWWP*VDTLPFPGPFPA

Parental  GPLAVAGGPRKTAAPVNALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPG
          GPLAVAGGPRK..APVNALVSHLLVVEPEKLYAMPDPAG.D.HLPA.ATLC.LF...IVVTIS..KSIPG
Retrocopy GPLAVAGGPRKI-APVNALVSHLLVVEPEKLYAMPDPAGSDAHLPAMATLCHLFH*KIVVTIS*TKSIPG

Parental  FSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQA
          F.SLSLSDQMSVL.S.WMEVLVLGVAQ.SLP.QDELAFAEDLVLDEEG..AAGLGELGA.LLQ.V..LQ.
Retrocopy F*SLSLSDQMSVL*SMWMEVLVLGVAQCSLPQQDELAFAEDLVLDEEGTLAAGLGELGAGLLQVVQ*LQG

Parental  LRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLL
          L.LE.E.Y.LLKALA.ANS.SVHI.D.EAVE.L.EALH.ALLEY.A.RAGP.G.AE..R.G.LLLTL.LL
Retrocopy LQLEQEGYILLKALAFANSGSVHIKDTEAVEKL*EALHVALLEYKASRAGPRGAAEWQREGMLLLTLLLL

Parental  RQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEAMMD
          .Q.AGKVLAH..GVKLE.K.PMHKLFLEML..MMD
Retrocopy HQRAGKVLAHLFGVKLESKAPMHKLFLEMLKSMMD

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	21.85 RPM
SRP051959_heart	0.00 RPM	14.08 RPM
SRP051959_kidney	0.00 RPM	24.67 RPM
SRP051959_liver	0.00 RPM	11.85 RPM
SRP051959_lung	0.00 RPM	6.62 RPM
SRP051959_lymph_node	0.00 RPM	7.47 RPM
SRP051959_skeletal_muscle	0.00 RPM	19.96 RPM
SRP051959_spleen	0.00 RPM	6.34 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3982 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3982 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3982 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018030	3 retrocopies	retro_cjac_3845, retro_cjac_3982 , retro_cjac_4023,
Callithrix jacchus	ENSCJAG00000020709	1 retrocopy	retro_cjac_3190,
Echinops telfairi	ENSETEG00000000262	1 retrocopy	retro_etel_733,
Homo sapiens	ENSG00000173153	2 retrocopies	retro_hsap_1171, retro_hsap_1237,
Gorilla gorilla	ENSGGOG00000001333	1 retrocopy	retro_ggor_970,
Macaca mulatta	ENSMMUG00000017803	1 retrocopy	retro_mmul_1275,
Nomascus leucogenys	ENSNLEG00000004971	2 retrocopies	retro_nleu_2855, retro_nleu_2856,
Pongo abelii	ENSPPYG00000003107	1 retrocopy	retro_pabe_63,
Pan troglodytes	ENSPTRG00000003833	1 retrocopy	retro_ptro_851,