RetrogeneDB ID: retro_cjac_329

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:33383137..33384526(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021808
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RUVBL2
• Ensembl ID: ENSCJAG00000000222
• Aliases: None
• Description: None

Sequence

>retro_cjac_329
ATGGCAACCGTGACAGCCACTAAAGCCCCGGAGATCCGCGATGTGACGAGGATTGAGCGAATTGGTGCTCACTCCCACAT
CCGGGGGCTGGGGCTGGACGATGCTTTGGAGCCTCGGCAGGCTTCCCAGGGCATGGTGGGTCAGCTGGCGGCACGGCGGG
CAGCAGGTGTGGTGCTGGAGATGATCCGGGAAGGGAAGATTGCCGGGCAGGCAGTTCTTATTGCTGGCCAGCCGGGCACA
GGGAAGACAGCCATCGCCATGGGCATGGCGCAGGCCCTGGGTCCGGACACGCCATTCACGGCAATTGCTGGCAGTGAAAT
CTTCTCCCTGGAGATGAGCAAGACCGAGGCGCTGACGCAGGCCTTCCGGAGGTCTATTGGCATTCGTATCAAGGAGGAGA
CAGAGATCATCGAAGGGGAGGTGGTGGAGATCCAGATTGATCGGCCGGCGACAAGGACGGGGTCCAAGGTGGGCAAACTG
ACCCTCAAGACGACAGAGATGGAGACCATCTACGACCTGGGCACCAAGACGATTGAGTCCCTGACCAAGGACAAGGTCCA
GGCCGGGGACATGATCACCATCGACAAGGCAACAGGCAAGATCTCCAAGCTGGGCCGCTCCTTCACACGCGCCCGAGACT
ACGATGCTATGGGCTCCCAGACCAAGTTCGTGCAGTGCCCAGATGGGGAGCTCCAGAAACGCAAGGAAGTGGTGCACACC
GTGTCCCTGCACGAGATTGACGTCATCAACTCCCGCACCCAGGGCTTCCTGGCGCTCTTCTCAGGTGACACAGGGGAGAT
CAAGTCAGAAGTTCGAGAGCAGATCCATGCCAAGGTGGCCGAGTGGCGCGAGGAGGGCAAGGCAGAGATCATCCCTGGGG
TGCTATTCATCGACGAGGTCCACATGCTGGACATTGAGAGCTTCTCCTTCCTCAACCAGGCCCTGGAGAGCGACATGGCA
CCTGTCCTGATCATGGCCACCAACCGCGGCATCACACGGATCCGGGGCACCAGCTACCAGAGCCCCCATGGTGTCCCCAT
CGATCTGCTGGACCGGCTGCTCATCGTCTCCACCACCCACTACAGCGAGAAAGACACAAAGCAGATCCTCCGCATCCGGT
GTGAGGAGGAAGATGTGGAGATGAGTGAGGACGCCTACACGGTGCTGACCCGCATCGGGCTGGAGACGTCACTGCGCTAT
GCCATCCAGCTTATCACGGCTGCCAGCCTGGTGTGCCGGAAACGCAAGGGCACAGAGGTACAGGTGGACGACATCAAGCA
GGTCTACTCACTCTTCCTGGACGAGTCCCGCTCCACGCAGTACATGAAGGAGTACCAGGACGCCTTCCTCTTCAATGAGC
TCAAAGGCGAGACCATGGATACCTCCTGA

Alignment

ORF - retro_cjac_329 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATVTATKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGR
          MATVTATK.PEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAG.
Retrocopy MATVTATKAPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGQ

Parental  AVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIEGE
          AVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIG.RIKEETEIIEGE
Retrocopy AVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGIRIKEETEIIEGE

Parental  VVEIQIDRPATGTGSKVGKLTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRSFTR
          VVEIQIDRPAT.TGSKVGKLTLKTTEMETIYDLGTK.IESLTKDKVQAGD.ITIDKATGKISKLGRSFTR
Retrocopy VVEIQIDRPATRTGSKVGKLTLKTTEMETIYDLGTKTIESLTKDKVQAGDMITIDKATGKISKLGRSFTR

Parental  ARDYDAMGSQTKFVQCPDGELQKRKEVVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVA
          ARDYDAMGSQTKFVQCPDGELQKRKEVVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQI.AKVA
Retrocopy ARDYDAMGSQTKFVQCPDGELQKRKEVVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQIHAKVA

Parental  EWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLL
          EWREEGKAEIIPGVLFIDEVHMLDIESFSFLN.ALESDMAPVLIMATNRGITRIRGTSYQSPHG.PIDLL
Retrocopy EWREEGKAEIIPGVLFIDEVHMLDIESFSFLNQALESDMAPVLIMATNRGITRIRGTSYQSPHGVPIDLL

Parental  DRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEV
          DRLLIVSTT.YSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEV
Retrocopy DRLLIVSTTHYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEV

Parental  QVDDIKRVYSLFLDESRSTQYMKEYQDAFLFNELKGETMDTS
          QVDDIK.VYSLFLDESRSTQYMKEYQDAFLFNELKGETMDTS
Retrocopy QVDDIKQVYSLFLDESRSTQYMKEYQDAFLFNELKGETMDTS

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	2.24 RPM	11.49 RPM
SRP051959_heart	2.33 RPM	9.51 RPM
SRP051959_kidney	2.00 RPM	11.38 RPM
SRP051959_liver	1.78 RPM	10.83 RPM
SRP051959_lung	1.69 RPM	10.80 RPM
SRP051959_lymph_node	1.42 RPM	9.34 RPM
SRP051959_skeletal_muscle	4.02 RPM	16.60 RPM
SRP051959_spleen	1.95 RPM	7.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_329 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_329 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_329 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000222	2 retrocopies	retro_cjac_329 , retro_cjac_4119,
Homo sapiens	ENSG00000183207	1 retrocopy	retro_hsap_4755,
Gorilla gorilla	ENSGGOG00000009245	1 retrocopy	retro_ggor_2961,
Macropus eugenii	ENSMEUG00000000069	1 retrocopy	retro_meug_2099,
Macaca mulatta	ENSMMUG00000003915	1 retrocopy	retro_mmul_2536,
Nomascus leucogenys	ENSNLEG00000004769	1 retrocopy	retro_nleu_1251,
Otolemur garnettii	ENSOGAG00000007519	2 retrocopies	retro_ogar_2473, retro_ogar_3246,
Pongo abelii	ENSPPYG00000010225	1 retrocopy	retro_pabe_3701,
Pan troglodytes	ENSPTRG00000011270	1 retrocopy	retro_ptro_3168,