RetrogeneDB ID: retro_cjac_3881

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285769.1:16863..17760(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LARP6
• Ensembl ID: ENSCJAG00000018642
• Aliases: None
• Description: None

Sequence

>retro_cjac_3881
ATGGCCCAGTCAGGCGGGGAGGCTCGGCCCGGGCCCGAGACGACGGTGCAGATCCGCGTCGCCATCCAGGAGGCCGAGGA
CGTGGACGAGCTGGAGGACGAGGGGGAGGGGGCGGAGACGCGGGGCGCGGGAGACCCTGCCCGGTACCTCAGCCCCGGCT
GGGGCAGCGCCAGCGAGGAGGAGCCGAGCCGCGGGCACAGTGGCACCACTGCAAGTGGAGGCGAGAATGAGCGTGAGGAC
CTGGAGCAGGAGTGGAAGCCCCCGGACGAGGAGTTAATCAAGAAACTGGTGGATCAGATCGAATTCTACTTCTCAGATGA
AAACCTGGAGAAGGACGCCTTTTTGCTAAAGCATGTGAGGAGGAACAAGCTGGGATATGTGAGCGTGAAGCTACTCACAT
CCTTCAAAAAGGTGAAACACCTTACACGGGACTGGAGAACCACAGCACATGCCTTGAAGTATTCAGTGGTCCTTGAGTTG
AATGAGGACCACCGGAAGGTGAGGAGGACCACCCCTGTCCCACTGTTCCCCAATGAGAACCTCCCCAGCAAGATGCTCCT
GGTCTATGATCTCTACCTGTCTCCCAAGCTCTGGGCTCTGGCCACCCCCCAGAAGAATGGAAGGGTACAGGAGAAGGTGA
TGGAACACCTGCTCAAGCTTTTCGGGAATTTTGGAGTCATCTCATCAGTGCGGATCCTCAAACCTGGGAGAGAGCTGCCC
CCTGACATCCGGAGGATCAGCAGCCGCTACAGCCAAGTGGGGACCCAGGAGTGTGCCATCGTGGAGTTTGAGGAGGTGGA
AGCCGCCATCAAAGCCCATGAGTTCATGATCACAGAATCTCAGGGCAAAGAGAACATGAAAGCTGTCCTGATTGGCATGA
AGCCACCCAAAAAGAAA

Alignment

ORF - retro_cjac_3881 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.33 %
• Parental protein coverage: 60.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQSGGEARPGPETTVQIRVAIQEAEDVDELEDEEEGAETRGAGDPARYLSPGWGSASEEEPSRGHSGTT
          MAQSGGEARPGPETTVQIRVAIQEAEDVDELEDE.EGAETRGAGDPARYLSPGWGSASEEEPSRGHSGTT
Retrocopy MAQSGGEARPGPETTVQIRVAIQEAEDVDELEDEGEGAETRGAGDPARYLSPGWGSASEEEPSRGHSGTT

Parental  ASGGENEREDLEQEWKPPDEELIKKLVDQIEFYFSDENLEKDAFLLKHVRRNKLGYVSVKLLTSFKKVKH
          ASGGENEREDLEQEWKPPDEELIKKLVDQIEFYFSDENLEKDAFLLKHVRRNKLGYVSVKLLTSFKKVKH
Retrocopy ASGGENEREDLEQEWKPPDEELIKKLVDQIEFYFSDENLEKDAFLLKHVRRNKLGYVSVKLLTSFKKVKH

Parental  LTRDWRTTAHALKYSVVLELNEDHRKVRRTTPVPLFPNENLPSKMLLVYDLYLSPKLWALATPQKNGRVQ
          LTRDWRTTAHALKYSVVLELNEDHRKVRRTTPVPLFPNENLPSKMLLVYDLYLSPKLWALATPQKNGRVQ
Retrocopy LTRDWRTTAHALKYSVVLELNEDHRKVRRTTPVPLFPNENLPSKMLLVYDLYLSPKLWALATPQKNGRVQ

Parental  EKVMEHLLKLFGTFGVISSVRILKPGRELPPDIRRISSRYSQVGTQECAIVEFEEVEAAIKAHEFMITES
          EKVMEHLLKLFG.FGVISSVRILKPGRELPPDIRRISSRYSQVGTQECAIVEFEEVEAAIKAHEFMITES
Retrocopy EKVMEHLLKLFGNFGVISSVRILKPGRELPPDIRRISSRYSQVGTQECAIVEFEEVEAAIKAHEFMITES

Parental  QGKENMKAVLIGMKPPKKK
          QGKENMKAVLIGMKPPKKK
Retrocopy QGKENMKAVLIGMKPPKKK

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	1.58 RPM
SRP051959_heart	0.02 RPM	12.38 RPM
SRP051959_kidney	0.00 RPM	3.24 RPM
SRP051959_liver	0.00 RPM	0.24 RPM
SRP051959_lung	0.00 RPM	6.59 RPM
SRP051959_lymph_node	0.00 RPM	1.07 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.71 RPM
SRP051959_spleen	0.00 RPM	2.75 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3881 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3881 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3881 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018642	1 retrocopy	retro_cjac_3881 ,
Monodelphis domestica	ENSMODG00000001314	2 retrocopies	retro_mdom_1273, retro_mdom_2018,