RetrogeneDB ID: retro_cjac_3190

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:19944015..19944855(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ESRRB
• Ensembl ID: ENSCJAG00000020709
• Aliases: None
• Description: None

Sequence

>retro_cjac_3190
ATGTCCTCGGATGACAGGCACCTGGGCTCCAGCTGCTGCTCCTTCATCAAGACTGAGCCGTCCAGCCCATCCTCCGGCAT
CGACGCCCTCAGCCGCAACAGCCCAGTGGCTCGTCCGACACCAGCAGCGGCTTTGGCCTGGCCCTCGGCACCCACACCAA
TAGTCTGGACTCACCACCCATGTTTGCAGGCGCCGGGCTGGGAAGCACCCCGTGCCGCAAGAGCTATGAGGACCATCCCA
CCGGCATCATGGAGGACTCGGCCATCAAGTGTGAGTACATGCTCAATGCCATCCCCAAGCACCTGTGCCTCGTGTGCGGG
GACATTGATACTGGCTACCACTATGGCGTGGCCTCCTGCAAGGCTTGCAAGGCCTTCTTCAAGAGGACCATTCAAGGGAA
CATCCAGTACAGCTGCCCGGCCACCAACGAGTACGAGATCACCAAACGGAGGCACAAGTCCTGCCAGGCCTGCCGCTTCA
TGAAATGCCTCAAAGTGGGGATGCCGAAGGAAGGTGTGCGCCTTGATCGAGTGCGTGGAGGCTGCCAATAATACAAGCGA
TGGGCTGGACTCAGAGAGCAGCCCATATCTGAGCTTACAAATTTCTCCACCTGCTAAAAAGCCATTGGTCAAGATTGTCT
CATACCTACTGGTGGCTGAGCCGGACAAGCTCTATGCCATGCCTCCCCCTGGCATGCCTGAGGGGGACATCAAGGCCCTG
ACCACTCTCTGTGACCTGGCAGACCGGGAGCTTGTGGTCCTCATTGGCTGGGCCAAACACATCCCAGGCTTCTTGAACCT
CTCCCTGGGGGACCAGATGAGCCTGCTGCAGAGTGCCTGG

Alignment

ORF - retro_cjac_3190 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.43 %
• Parental protein coverage: 55.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSDDRHLGSSCGSFIKTEPSSPSSGIDALSHHSP-SGSSDASGGFGLALGTHANGLDSPPMFAGAGLGG
          MSSDDRHLGSSC.SFIKTEPSSPSSGIDALS..SP.SGSSD.S.GFGLALGTH.N.LDSPPMFAGAGLG.
Retrocopy MSSDDRHLGSSCCSFIKTEPSSPSSGIDALSRNSP<SGSSDTSSGFGLALGTHTNSLDSPPMFAGAGLGS

Parental  TPCRKSYEDCASGIMEDSAIKCEYMLNAIPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSC
          TPCRKSYED...GIMEDSAIKCEYMLNAIPK.LCLVCGDI..GYHYGVASC.ACKAFFKRTIQGNI.YSC
Retrocopy TPCRKSYEDHPTGIMEDSAIKCEYMLNAIPKHLCLVCGDIDTGYHYGVASCKACKAFFKRTIQGNIQYSC

Parental  PATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKR-RLDSESSPYLSLQISPPAKKP
          PATNE.EITKRR.KSCQACRFMKCLKVGM.KEGVRLDRVRGG.Q.YKR..LDSESSPYLSLQISPPAKKP
Retrocopy PATNEYEITKRRHKSCQACRFMKCLKVGMPKEGVRLDRVRGGCQ*YKR>GLDSESSPYLSLQISPPAKKP

Parental  LTKIVSYLLVAEPDKLYAMPPPGMPEGDIKALTTLCDLADRELVVIIGWAKHIPGFSNLSLGDQMSLLQS
          L.KIVSYLLVAEPDKLYAMPPPGMPEGDIKALTTLCDLADRELVV.IGWAKHIPGF.NLSLGDQMSLLQS
Retrocopy LVKIVSYLLVAEPDKLYAMPPPGMPEGDIKALTTLCDLADRELVVLIGWAKHIPGFLNLSLGDQMSLLQS

Parental  AW
          AW
Retrocopy AW

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	0.44 RPM
SRP051959_heart	0.30 RPM	1.58 RPM
SRP051959_kidney	0.00 RPM	2.73 RPM
SRP051959_liver	0.74 RPM	0.00 RPM
SRP051959_lung	0.07 RPM	0.08 RPM
SRP051959_lymph_node	0.02 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.04 RPM	3.43 RPM
SRP051959_spleen	0.13 RPM	0.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3190 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3190 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3190 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 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 ,
Mus musculus	ENSMUSG00000021255	1 retrocopy	retro_mmus_3461,
Rattus norvegicus	ENSRNOG00000010259	1 retrocopy	retro_rnor_2876,
Tursiops truncatus	ENSTTRG00000001302	1 retrocopy	retro_ttru_139,