RetrogeneDB ID: retro_cjac_3845

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285001.1:5666..6922(-)
• Located in intron of: ENSCJAG00000010890

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_3845
ATGTCCAGCCAGGTGGTGGGAATTGAGCCTCTTCATATCAAGGCAGAGCTGACCAGTCCTGACAGTCCAAAGTGTTCCTC
AGAGATAGAGACTGAGCCACCTGTGGTCGTGGCCCCTGGTCCAGCTCCCACCCACTGCCTCCCAGGCCATAAGGAAGAGG
AGGATGGGAAGGGGGCTGCACCTGGCAAGCAGGGCAGTGGGAAGCTGGTGCTCAGCCCCCTGCCTAATTGCCTCTGCCTG
GCCTGTGGGGACGTGGCCTCTGGCTACTACTATGATGTGGCATCCTGTGAAGCCTGCAAAGCCTTCTTCAAGAGGACCAT
CCAGAGGAGCATCCAGTACAGCTGTCTGGCTTCCAATGAGTGTGAGATCACCAAGCAGAGACTCAAGGCCTGCCACTTTA
CCAAGTGCCTGTGGGTGGGCATGCTTAAGAAGGGAGTACACCTGGACTGCATCAGAGATGGGCGGCAGAAGTACAAGCGA
TGGCCAGAGGTGGACCCACTGCCCTTCCCAGGCCCCTTCCCTGCTGTGACCCTGGCAGTAGCTGGAGGGCCTCAGAAGAC
AGCCCCAGTGAATGCCCTGGTGTCTCATCTGCTGGTGGTTGAGCCTGAGAAGCTCTATGCCATGCTTGACCTGTGGGCCC
TTATGGGCAGCTCCCAGCCATGGCTACCTTCTGTCACTTCTTTCACCAAGAGATCATGGTCACCATCAGCTGGACCAAGA
GCATACCAGGCTTCTCATTGCTGTCGCTGTCTGACCAAATATCAGTACTGTAGAGCATGTGGATGGATGTGCTGGTGCTG
GGTGTGGCCCAGCACTCACTGCCAATGCAGGATGAGCTGGCCTTTGCTGAGGACTTAGTGCTGGATAAAGAGGAGGCTCT
GGCAGCTGGTCTGGGGGAACTGGGGGCTGCCCTGCTGCAGCTGGTGCAGTGACTGCAGGCTCTACGGCTGGAGCAAGAGG
AGTACATCCTCCCGAAGGCCCCGGCCCTTGCCAATTCAGACTCTGTGCACATCAAAGATACCAAGGCTATGGATCAGCTG
TGATAATGCCTGCATGAGGCCCTGCTGGAGTACAAAGCCAGCCGGGCTGGCCCCAGATGATCTGCTGAGTAGCAGTGGGT
GGGCAGGCTGCTGCTCACACTAATGCTCCTTCACCAGACAGTGAGCAAAGTGCTGGCCCATCTCTATGGGGTGAAGCTGG
AGAGCAAGGCACCCATGCACAAGCTGTTCTTGGAGATGCTAAAGGCCATGATGGAC

Alignment

ORF - retro_cjac_3845 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.3 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSQVVGIEPLYIKAEPASPDSPKGSSETETEPPVTLAPGPAPTRCLPGHKEEEDGEGAGPGEQGGGKLV
          MSSQVVGIEPL.IKAE..SPDSPK.SSE.ETEPPV..APGPAPT.CLPGHKEEEDG.GA.PG.QG.GKLV
Retrocopy MSSQVVGIEPLHIKAELTSPDSPKCSSEIETEPPVVVAPGPAPTHCLPGHKEEEDGKGAAPGKQGSGKLV

Parental  LSSLPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCPASNECEITKRRRKACQACRFTKCL
          LS.LP..LCL.CGDVASGY.Y.VASCEACKAFFKRTIQ.SI.YSC.ASNECEITK.R.K...AC.FTKCL
Retrocopy LSPLPNCLCLACGDVASGYYYDVASCEACKAFFKRTIQRSIQYSCLASNECEITKQRLK---ACHFTKCL

Parental  RVGMLKEGVRLDRVRGGRQKYKRRPEVDPLPFPGPFPAGPLAVAGGPRKTAAPVNALVSHLLVVEPEKLY
          .VGMLK.GV.LD..R.GRQKYKR.PEVDPLPFPGPFPA..LAVAGGP.KTA.PVNALVSHLLVVEPEKLY
Retrocopy WVGMLKKGVHLDCIRDGRQKYKRWPEVDPLPFPGPFPAVTLAVAGGPQKTA-PVNALVSHLLVVEPEKLY

Parental  AMPD-PAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLP
          AM.D.P.GP.G.LPA.AT.C..F..EI.VTISW.KSIPGFS.LSLSDQ.SVL.S.WM.VLVLGVAQ.SLP
Retrocopy AMLD<PVGPYGQLPAMATFCHFFHQEIMVTISWTKSIPGFSLLSLSDQISVL*SMWMDVLVLGVAQHSLP

Parental  LQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVE
          .QDELAFAEDLVLD.E.A.AAGLGELGAALLQLV..LQALRLE.EEY.L.KA.ALANSDSVHI.D..A..
Retrocopy MQDELAFAEDLVLDKEEALAAGLGELGAALLQLVQ*LQALRLEQEEYILPKAPALANSDSVHIKDTKAMD

Parental  QLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLE
          QL...LHEALLEY.A.RAGP...AE....GRLLLTL.LL.QT..KVLAH.YGVKLE.K.PMHKLFLEML.
Retrocopy QL**CLHEALLEYKASRAGPR*SAE*QWVGRLLLTLMLLHQTVSKVLAHLYGVKLESKAPMHKLFLEMLK

Parental  AMMD
          AMMD
Retrocopy AMMD

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	0.02 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_3845 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3845 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3845 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,