RetrogeneDB ID: retro_cjac_3415

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01178768.1:6267..7115(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000034693
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COQ5
• Ensembl ID: ENSCJAG00000001205
• Aliases: None
• Description: coenzyme Q5 homolog, methyltransferase (S. cerevisiae) [Source:HGNC Symbol;Acc:28722]

Sequence

>retro_cjac_3415
AAAGAGAAGCAGGTAACGGAAACTCACTTTGGGTTTCAGACTGTGTCGGAAGAGAAAAAGTGGGGCAAAGTCCATCAGGT
GTTTGAAAGTGTGGCTAAGAAGTATGATGTGATGAATGATATGATGAGTCTTGGTATCCATCCTCTTTGGAAGGATTTAC
TGCTCTGGAATATACATCCACTTCCTGGGACCCAGCTGCTTGATGTTGCTGGAGGCACAGGTGACATTGCATTCCGGTTC
CTAAATTATGTTCAGTCCCAGCATCAGAGAAAACAGAAGAGTCAGTTAAGGGACCAACAAAGTTTATCCTGGGAAGAAAT
TGCCAAAGAGTACCAGAATGAAGAAGATTCCTTGGGTGGGTCTCATGTCATGGTGTGTGACATCAACAAGGAGATGCTAA
AGGTTGGAAAGCAGAAAGCCTTGGCTCAAGGATACAGAGCTGGACTTGCATGGGTATTAGGAGATGCCGAAGAACTTCCC
TTTGATGATGACAAGTTTGATATTTACACCATTGCCTTTGGGCTTCGGAATGTCACACACATTGATCAGGCACTCCAGGA
AGCCCATCGGGTACTGAAACCAGGAGGACGGTTTCTGTGTCTGGAATTTAGCCAAGTGAACAATCCCCTCATATCCAGGC
ATTATGATCTATATAGCTTCCAGGTCATCCCTGTCCTGGAGAGGTCATTGCTGGAGACTGGAAGTCCTATCAATACCTTG
TAGAGAGTATCCAAATGTTCCTGTCTCAGAAAGAGTTCAAGGAGATGATAGAAGATGCAGGCTTTCACAAGGCCACTTAT
GAAAGTCTAACATCAGGCATTGTGGCCATTCATTCTGCCTTCAAACTT

Alignment

ORF - retro_cjac_3415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.66 %
• Parental protein coverage: 86.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QEKRATETHFGFQTVSEEEKGGKVHQVFESVAKKYDVMNDMMSLGIHRLWKDLLLWKMHPLPGTQLLDVA
          .EK..TETHFGFQTVSEE.K.GKVHQVFESVAKKYDVMNDMMSLGIH.LWKDLLLW..HPLPGTQLLDVA
Retrocopy KEKQVTETHFGFQTVSEEKKWGKVHQVFESVAKKYDVMNDMMSLGIHPLWKDLLLWNIHPLPGTQLLDVA

Parental  GGTGDIAFRFLNYVQSQHQRKQKRQLRAQQSLSWEEIAKEYQNEEDSLGGSHVMVCDINKEMLKVGKQKA
          GGTGDIAFRFLNYVQSQHQRKQK.QLR.QQSLSWEEIAKEYQNEEDSLGGSHVMVCDINKEMLKVGKQKA
Retrocopy GGTGDIAFRFLNYVQSQHQRKQKSQLRDQQSLSWEEIAKEYQNEEDSLGGSHVMVCDINKEMLKVGKQKA

Parental  LAQGYRAGLAWVLGDAEELPFDDDKFDIYTIAFGIRNVTHIDQALQEAHRVLKPGGRFLCLEFSQVNNPL
          LAQGYRAGLAWVLGDAEELPFDDDKFDIYTIAFG.RNVTHIDQALQEAHRVLKPGGRFLCLEFSQVNNPL
Retrocopy LAQGYRAGLAWVLGDAEELPFDDDKFDIYTIAFGLRNVTHIDQALQEAHRVLKPGGRFLCLEFSQVNNPL

Parental  ISRLYDLYSFQVIPVL-GEVIAGDWKSYQYLVESIRRFPSQEEFKEMIEDAGFHKVTYESLTSGIVAIHS
          ISR.YDLYSFQVIPVL.GEVIAGDWKSYQYLVESI..F.SQ.EFKEMIEDAGFHK.TYESLTSGIVAIHS
Retrocopy ISRHYDLYSFQVIPVL<GEVIAGDWKSYQYLVESIQMFLSQKEFKEMIEDAGFHKATYESLTSGIVAIHS

Parental  AFKL
          AFKL
Retrocopy AFKL

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	3.95 RPM
SRP051959_heart	0.04 RPM	15.65 RPM
SRP051959_kidney	0.00 RPM	13.49 RPM
SRP051959_liver	0.00 RPM	11.68 RPM
SRP051959_lung	0.00 RPM	5.61 RPM
SRP051959_lymph_node	0.00 RPM	7.15 RPM
SRP051959_skeletal_muscle	0.02 RPM	12.14 RPM
SRP051959_spleen	0.00 RPM	6.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3415 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3415 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3415 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001205	4 retrocopies	retro_cjac_1277, retro_cjac_3050, retro_cjac_3383, retro_cjac_3415 ,
Microcebus murinus	ENSMICG00000006371	1 retrocopy	retro_mmur_1327,
Tupaia belangeri	ENSTBEG00000009255	1 retrocopy	retro_tbel_3288,