RetrogeneDB ID: retro_cjac_3212

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:40766610..40767484(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERI3
• Ensembl ID: ENSCJAG00000003995
• Aliases: None
• Description: ERI1 exoribonuclease family member 3 [Source:HGNC Symbol;Acc:17276]

Sequence

>retro_cjac_3212
CATTGGGGCTTTCCAGCTTTCACAGAACCTTCAGCATCCCCAGCTGCCGGTCTTGGGATCTTCGAAGTAAGGAGAGTTTT
AGATGCTTCTGGATGTTCAATGCTAGCACCTTTACGACTGGAGCAGCTCGATTTTCTTCATATTTACTTTCAAGAGCAAG
AAAAGTGCTGGGCTCGCACTTATATTCTCCCTGTGGTATTCCGGAGTTCTGTTCCATATCCACCAGAAAGCTGGCAGCCC
ACGGCTTTGGCGCATCCATGGCGGCAATGGTGTCCTTCCCTCCCCAGAGGTATCACTACTTTTTAGTGCTGGATTTTGAG
CCCACATGCGACAAGCCACAGATTCATCCTCAGGAAATCACTGAGTTCCCCATCCTGAAGCTAAATGGCCGGACCATGGA
GATTGAGTCTACCCTTCACATGTATGTCCAGCCTGTAGTCCATCCACAGCTTACCCCTTCTGTACAGAGCTCACCGGGAT
TATTCAAGCTATGGTGGATGGTTAGCCAAGCCTGCAGCAAGTGCTGGAGAGAGTCAATGAGTGGATGGCGAAGGAAGGCC
TCTTAGATCCACACATCAAGTCAATTTTTGTCACCTGTGGAGCCTGGGACTTAAAAGTCATGCTCCCGGGCCAGTGCCGG
TATTTGGGCTTACCAGTGGCGGATTGCTTCAAGCAGTGGATTAATCTGAAAAAGGCTTACAGCTTCGCCATGAGCTGCTG
GCCCAAGAATGGACTTCTAGACATGAATAAGGGCCTCAGCCTGCAACACACAGGCCAGCCCCACAGCGGCATTGACGACT
GCAAGAACATTGCCAACATCATGGAGACACTCGCCTACCGAGGCTTCATCTTCAAGCAGACATCGAAACCATTC

Alignment

ORF - retro_cjac_3212 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.54 %
• Parental protein coverage: 86.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HWGFPAFTEPSASPAAGLGIFEVRRVLDASGCSMLAPLQ-TGAARFSSYLLSRARKVLGSHLFSPCGVPE
          HWGFPAFTEPSASPAAGLGIFEVRRVLDASGCSMLAPL..TGAARFSSYLLSRARKVLGSHL.SPCG.PE
Retrocopy HWGFPAFTEPSASPAAGLGIFEVRRVLDASGCSMLAPLR<TGAARFSSYLLSRARKVLGSHLYSPCGIPE

Parental  FCSISTRKLAAHGFGASMAAMVSFPPQRYHYFLVLDFEATCDKPQIHPQEIIEFPILKLNGRTMEIESTF
          FCSISTRKLAAHGFGASMAAMVSFPPQRYHYFLVLDFE.TCDKPQIHPQEI.EFPILKLNGRTMEIEST.
Retrocopy FCSISTRKLAAHGFGASMAAMVSFPPQRYHYFLVLDFEPTCDKPQIHPQEITEFPILKLNGRTMEIESTL

Parental  HMYVQPVVHPQLTP-FCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVM
          HMYVQPVVHPQLTP.FCTELTGIIQAMVDG.PSLQQVLERV.EWMAKEGLLDP..KSIFVTCG.WDLKVM
Retrocopy HMYVQPVVHPQLTP<FCTELTGIIQAMVDG*PSLQQVLERVNEWMAKEGLLDPHIKSIFVTCGAWDLKVM

Parental  LPGQCQYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTL
          LPGQC.YLGLPVAD.FKQWINLKKAYSFAM.CWPKNGLLDMNKGLSLQH.G.PHSGIDDCKNIANIM.TL
Retrocopy LPGQCRYLGLPVADCFKQWINLKKAYSFAMSCWPKNGLLDMNKGLSLQHTGQPHSGIDDCKNIANIMETL

Parental  AYRGFIFKQTSKPF
          AYRGFIFKQTSKPF
Retrocopy AYRGFIFKQTSKPF

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	0.07 RPM	5.64 RPM
SRP051959_heart	0.16 RPM	10.63 RPM
SRP051959_kidney	0.62 RPM	21.83 RPM
SRP051959_liver	0.02 RPM	11.70 RPM
SRP051959_lung	1.19 RPM	8.31 RPM
SRP051959_lymph_node	0.11 RPM	5.59 RPM
SRP051959_skeletal_muscle	0.02 RPM	18.19 RPM
SRP051959_spleen	0.29 RPM	6.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3212 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3212 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3212 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015559	1 retrocopy	retro_btau_1015,
Callithrix jacchus	ENSCJAG00000003995	1 retrocopy	retro_cjac_3212 ,
Callithrix jacchus	ENSCJAG00000009400	1 retrocopy	retro_cjac_2424,
Felis catus	ENSFCAG00000005285	1 retrocopy	retro_fcat_1768,
Pan troglodytes	ENSPTRG00000000655	1 retrocopy	retro_ptro_899,