RetrogeneDB ID: retro_cjac_4024

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL289415.1:7884..8544(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYD88
• Ensembl ID: ENSCJAG00000010193
• Aliases: None
• Description: myeloid differentiation primary response 88 [Source:HGNC Symbol;Acc:7562]

Sequence

>retro_cjac_4024
CAGCCAGCCATGGCTGCAGAAGGTCCCAGCGCAGGGTCTGTGGCCCCGGTCTCCTCCACATCCTCCCTGCCCCTGGCTGC
TCTCAACATGCGAGTGCGGCGCCGCCTGTCGCTGTTCTTGAACGTGCAGACGCAGGTGGCAGCCGACAGGACCGTGCTAG
TGGAGGTGATGGACTTTGAGTACTTGGAGATCTGGTAGCTGGAATCGCACGCCAACCCCACGGGCAGGCTGCTGGACGCC
TGGCAGGGACACCCCGGTGCCTCGGTAGGCCGACTGCTGGAGCTGCTCACCAAGCTGGGTCACGGCGATGTGCTGCTGGA
GATTGAGGTGGATTGCCAAAAGTATATCTTGAAGCAGCAGCAGGAGGAGGCTGAAAAGCCCTTACAGGTGGCCTCTGTCA
ACAGCAGTGTACCATGGACAACAGAGCTGGCAGGCATCACCACACTTGACGACCCCCTGGCGCAAATGCCTGAGCGTTTC
AAGGCCTTCATCTGTTATTGCCCCAGCGACATCCAGTTTGTGCAGGAGATGATCCGGCAACTGGAACAGACAAACTATAG
ACTGAAGTTATGTGTATCTGGCCGCGATGTCCTGCCTGGCACCTGTGTCTGGTCTATTGCTAGTGAGCTCAGCGAGAAAA
GGTACCGCAGGATGGTGATT

Alignment

ORF - retro_cjac_4024 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.84 %
• Parental protein coverage: 72.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QPAMAAEGPGAGSVTPVSSTSSLPLAALNMRVRRRLSLFLNVRTQVAADWTVLAEEMDFEYLEIRQLESH
          QPAMAAEGP.AGSV.PVSSTSSLPLAALNMRVRRRLSLFLNV.TQVAAD.TVL.E.MDFEYLEI..LESH
Retrocopy QPAMAAEGPSAGSVAPVSSTSSLPLAALNMRVRRRLSLFLNVQTQVAADRTVLVEVMDFEYLEIW*LESH

Parental  ADPTGRLLDAWQGRPGASVGRLLELLTKLGRDDVLLELGPSIEEDCQKYILKQQQEEAEKPLQVASVDSS
          A.PTGRLLDAWQG.PGASVGRLLELLTKLG..DVLLE....IE.DCQKYILKQQQEEAEKPLQVASV.SS
Retrocopy ANPTGRLLDAWQGHPGASVGRLLELLTKLGHGDVLLE----IEVDCQKYILKQQQEEAEKPLQVASVNSS

Parental  VPRTTELAGITTLDDPLGQMPERFDAFICYCPSDIQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSI
          VP.TTELAGITTLDDPL.QMPERF.AFICYCPSDIQFVQEMIRQLEQTNYRLKLCVS.RDVLPGTCVWSI
Retrocopy VPWTTELAGITTLDDPLAQMPERFKAFICYCPSDIQFVQEMIRQLEQTNYRLKLCVSGRDVLPGTCVWSI

Parental  ASELIEKRCRRMVV
          ASEL.EKR.RRMV.
Retrocopy ASELSEKRYRRMVI

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	15.31 RPM
SRP051959_heart	0.00 RPM	4.63 RPM
SRP051959_kidney	0.02 RPM	4.86 RPM
SRP051959_liver	0.02 RPM	9.44 RPM
SRP051959_lung	0.02 RPM	18.24 RPM
SRP051959_lymph_node	0.00 RPM	16.16 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.64 RPM
SRP051959_spleen	0.02 RPM	22.44 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4024 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4024 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4024 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010193	1 retrocopy	retro_cjac_4024 ,