RetrogeneDB ID: retro_cjac_3933

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286325.1:13648..14142(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000003712
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LMO4
• Ensembl ID: ENSCJAG00000007385
• Aliases: None
• Description: LIM domain only 4 [Source:HGNC Symbol;Acc:6644]

Sequence

>retro_cjac_3933
ATGATGAATCCGGGCAGCAGCTAGCAGCAGCCCCTGGTGACGGCCGGCTCCCTCTCCTGGAGGCGGTGCGCAGGCTGCGG
GGGCAAGATTGCGGACCGTTTCTGCTCTATGCCATGGACAGCTACTGGCACAGCCGGTGCCTCAAGTGCTCCTGCTGCCA
GGCGCAACTGGGCGACATCGGCATGTCCTGTTACACCAAGAGCGGCATGATCCTTTGCAGAAATGACTACATTAGGTTAT
TTGGGAATAGCGGTGCTTGCAGCGCTTGTGGACAGTCGATTCCTGGGAGCGAACTCGTCATAAGGGCGCAAGGCAATGTG
TATCATCTTAAGTGTTTTACATGCTCTACCTGCCGGAATCGCCTGGTCCCGGGAGATCGGTTTCACTACATCAATTTCAG
TTTATTTTGTGAACATAATAGACCTACAGCTCTCATCAATGGCCATTTGAATTTACTTCAGAGCAATCCTCTACTGCCAG
ACCAGAAGGTCTGC

Alignment

ORF - retro_cjac_3933 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVNPGSSSQPPPVTAGSLSWKRCAGCGGKIADRF-LLYAMDSYWHSRCLKCSCCQAQLGDIGTSCYTKSG
          M.NPGSS.Q.P.VTAGSLSW.RCAGCGGKIADRF.LLYAMDSYWHSRCLKCSCCQAQLGDIG.SCYTKSG
Retrocopy MMNPGSS*QQPLVTAGSLSWRRCAGCGGKIADRF<LLYAMDSYWHSRCLKCSCCQAQLGDIGMSCYTKSG

Parental  MILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEH
          MILCRNDYIRLFGNSGACSACGQSIP.SELV.RAQGNVYHLKCFTCSTCRNRLVPGDRFHYIN.SLFCEH
Retrocopy MILCRNDYIRLFGNSGACSACGQSIPGSELVIRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINFSLFCEH

Parental  DRPTALINGHLNSLQSNPLLPDQKVC
          .RPTALINGHLN.LQSNPLLPDQKVC
Retrocopy NRPTALINGHLNLLQSNPLLPDQKVC

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	0.02 RPM	8.10 RPM
SRP051959_heart	0.00 RPM	10.28 RPM
SRP051959_kidney	0.02 RPM	12.56 RPM
SRP051959_liver	0.00 RPM	1.80 RPM
SRP051959_lung	0.02 RPM	9.26 RPM
SRP051959_lymph_node	0.02 RPM	11.80 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.99 RPM
SRP051959_spleen	0.00 RPM	6.28 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3933 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3933 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3933 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000305	1 retrocopy	retro_btau_1276,
Callithrix jacchus	ENSCJAG00000007385	1 retrocopy	retro_cjac_3933 ,