RetrogeneDB ID: retro_cjac_4023

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL288880.1:2589..3773(+)
• 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_4023
ATGTCTAGCCAGGTGGTGGGCATTAAGCCTCTCTACATCAAGGCAGAACCGGCCAGCCCTGACAATCCAAAGGTTTCCGC
AGAGATGGAGACCGAGCCTCCTGTGGCCCTGCTCCCTGGTTCAGCTCCCACCCGCTGCCTCCCAGGCCATAAGGAAGAGG
AGGATGGGGAGGGGGCTGGGCCTGGCGAGCAGGGTAGTGGGAAGTTGGTGTTCAGCTCCCTGCCCAAGCACCTCTGCCTG
GCCTATGGGAACGTGGCCTTCAGATACCACTATGGTGTGGCATCCTGTGAGGCCTGCAAAGCCTTCTTCAAGACGACCAT
TCAGGGGAGCATCGAGTACAGCTGTCTGGCTTCCAATGAGTGTGAGATCACCAAGTGGAGAGGCAAGGCCTACCAGGCTT
GCCGCTTCACCAAGTGCCTGTGGGTGGGCATGCTCAGTGAGAGAGTGCACTTGGACCACATCTGGGATGGGCAGCAGAAG
TACAAGCAGTGGCCAGAGGTGGACCCACTGCCCTTCCCAGGCCCCTTCCCTGCTGGGCCCCTGGTAGTAGCTGGAGGACC
TCGGAAGGCAGCCCCAGTGAATGCACTGGTGTCTCATCTGCTGGTGGTTGAGCCTGAGAAGCTCTATGCCATGCCTGACC
CCGCAGGCCCTGATGGGCACCTCCCAGCCATGGCTACCCTCTGACACCTCTTTGATTGAGAGATTGTGGTCACCATCAGC
TGGGCCAAGAGCACACCAGGCTTCTCATCGCTGTTGCTATCTGACCAGCAGTCAGTACTGCAGAGCGTGTGGACAGAGGT
GCCGGTGCTGCGTGTGGCCCAGCGCTCTCTGCCACAGCAGGATGAGCTGGCCTTTCCTGAGGACTTAGTCCTGGATGAAG
AGGGGGCTCTGGCATTTGGTCTGGGGGAAATGGGGCTGCCCTCCTGCAGCTGGTGCAGCGACAGCAGGCTCTCTGGCTGG
AGAAAGAGGAGTACATCCTCCTGAAGGCCCTGGCCCTTGCCAATTCAGCCTCTGTGCACATTGAAAATGCTGAGGCTGAG
GAACAGCTGTGAACAGCCCTGTACGATGCCCTGCTGGAGTACAAAGCCAGCTGGGCTGGCCCGGGAGGGGGTGCTGAGCA
GTGGCAGGTGGGCAGGCTGCTTCTCACACTACCACTCCTCTGCCAGACAGGGGGCCCATCTCTA

Alignment

ORF - retro_cjac_4023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.61 %
• Parental protein coverage: 93.62 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSQVVGIEPLYIKAEPASPDSPKGSSETETEPPVTLAPGPAPTRCLPGHKEEEDGEGAGPGEQGGGKLV
          MSSQVVGI.PLYIKAEPASPD.PK.S.E.ETEPPV.L.PG.APTRCLPGHKEEEDGEGAGPGEQG.GKLV
Retrocopy MSSQVVGIKPLYIKAEPASPDNPKVSAEMETEPPVALLPGSAPTRCLPGHKEEEDGEGAGPGEQGSGKLV

Parental  LSSLPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCPASNECEITKRRRKACQACRFTKCL
          .SSLPK.LCL..G.VA..YHYGVASCEACKAFFK.TIQGSIEYSC.ASNECEITK.R.KA.QACRFTKCL
Retrocopy FSSLPKHLCLAYGNVAFRYHYGVASCEACKAFFKTTIQGSIEYSCLASNECEITKWRGKAYQACRFTKCL

Parental  RVGMLKEGVRLDRVRGGRQKYKRRPEVDPLPFPGPFPAGPLAVAGGPRKTAAPVNALVSHLLVVEPEKLY
          .VGML.E.V.LD....G.QKYK..PEVDPLPFPGPFPAGPL.VAGGPRK.AAPVNALVSHLLVVEPEKLY
Retrocopy WVGMLSERVHLDHIWDGQQKYKQWPEVDPLPFPGPFPAGPLVVAGGPRK-AAPVNALVSHLLVVEPEKLY

Parental  AMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPL
          AMPDPAGPDGHLPA.ATL..LFD.EIVVTISWAKS.PGFSSL.LSDQ.SVLQSVW.EV.VL.VAQRSLP.
Retrocopy AMPDPAGPDGHLPAMATL*HLFD*EIVVTISWAKSTPGFSSLLLSDQQSVLQSVWTEVPVLRVAQRSLPQ

Parental  QDELAFAEDLVLDEEGARAAGLGEL-GAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVE
          QDELAF.EDLVLDEEGA.A.GLGE..GAALLQLV.R.QAL.LE.EEY.LLKALALANS.SVHIE.AEA.E
Retrocopy QDELAFPEDLVLDEEGALAFGLGEM<GAALLQLVQRQQALWLEKEEYILLKALALANSASVHIENAEAEE

Parental  QLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVL
          QL..AL..ALLEY.A..AGPGGGAE....GRLLLTLPLL.QT.G..L
Retrocopy QL*TALYDALLEYKASWAGPGGGAEQWQVGRLLLTLPLLCQTGGPSL

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	0.02 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_4023 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4023 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4023 has 0 orthologous retrocopies within eutheria group .

---

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,