RetrogeneDB ID: retro_cjac_3050

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:20851352..20852332(+)
• Located in intron of: None

Retrocopy information

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

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_3050
ATGGCGGCTCCCAGAAGCTTGGCTCTATGGAACTATTGCAGTCGTAGGTGGTTGCAGGCGATGCGGGGCTGTCACCTCCT
CGGAGTTCATGGCTCTTCGCCCAGGGCCCCACTAAGTGTGCGGCTCTTGTCCCAAGAGAAGTGGGGAACAGAAATGCACT
TCGGGTTTCAGACTGTGTCGGAAGAGGAAAAGGGGGGCAAAGTCCATCAGGTGTTTGAAAGTGTGCCTAAGAAGTATGAT
GTGATGAATAATATGATGAGTCTTGGTATCCATCATCTTTGGAAGGATTTGGTGCTCTGGAAGATGCATCTGCTTCCTGG
AACCCAGCTGCTTGATGTTGCTGGAGGCACAGGTGACATTGGATTCCGGTTCTTAAATTATGTTTAGTCCCAGCATCAGA
GAAAACAGAAGAGGCAGTTAAGGGCCCAACAAAGTTTATCCTGGGAAGAAATTGCCAAAGAGTACCAAAATGAAGAAGAT
TCCTTGGGCGGGTCTCATGTCATGGTGTGTGACATCAACAAGGAGATGCTAAAGGCTGGAAAGCAGAAAGTCTTGGCTCA
AGGATACAGAGCTGGACTTGCATGGGTATTAGGAGATGCCGAAGAACTGCCCTTTGATGATGACAAGTTTGACATTTACA
CCATTGCCTTTGGGATTCAGAATGTCACACACATTGGTCAGGCAACCCAGGAAGCCCATTGGGTGCTAAAACCAGGAGGA
TGGTTTCTGTGTCTGGAGTTTAGCCAAGTGAACAATCCCCTCATATCCAGGCTTTATGACCTATATAGCTTCCAGGTCAT
CCCTGTCCTGGGAGAGGTCATTGCTGGAGACTGAAAGTCCTATCAACCCTTGTAGAGAGTATCCAAAGGTTTCTGTCTCA
GGAAGAGTTCAAGGAGATGATAGAAGGTGCAGGCTTTCACAAGGTCACTTATGATAGCCTAACATCAGGCATGTTGGCCA
TTCATTCTGCCTTCAAACTT

Alignment

ORF - retro_cjac_3050 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.63 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAPRSLALWNYCSRRWSRAMRGCQLLGLRGSWPEAPLSARLLSQEKRATETHFGFQTVSEEEKGGKVHQ
          MAAPRSLALWNYCSRRW..AMRGC.LLG..GS.P.APLS.RLLSQEK..TE.HFGFQTVSEEEKGGKVHQ
Retrocopy MAAPRSLALWNYCSRRWLQAMRGCHLLGVHGSSPRAPLSVRLLSQEKWGTEMHFGFQTVSEEEKGGKVHQ

Parental  VFESVAKKYDVMNDMMSLGIHRLWKDLLLWKMHPLPGTQLLDVAGGTGDIAFRFLNYVQSQHQRKQKRQL
          VFESV.KKYDVMN.MMSLGIH.LWKDL.LWKMH.LPGTQLLDVAGGTGDI.FRFLNYV.SQHQRKQKRQL
Retrocopy VFESVPKKYDVMNNMMSLGIHHLWKDLVLWKMHLLPGTQLLDVAGGTGDIGFRFLNYV*SQHQRKQKRQL

Parental  RAQQSLSWEEIAKEYQNEEDSLGGSHVMVCDINKEMLKVGKQKALAQGYRAGLAWVLGDAEELPFDDDKF
          RAQQSLSWEEIAKEYQNEEDSLGGSHVMVCDINKEMLK.GKQK.LAQGYRAGLAWVLGDAEELPFDDDKF
Retrocopy RAQQSLSWEEIAKEYQNEEDSLGGSHVMVCDINKEMLKAGKQKVLAQGYRAGLAWVLGDAEELPFDDDKF

Parental  DIYTIAFGIRNVTHIDQALQEAHRVLKPGGRFLCLEFSQVNNPLISRLYDLYSFQVIPVLGEVIAGDWKS
          DIYTIAFGI.NVTHI.QA.QEAH.VLKPGG.FLCLEFSQVNNPLISRLYDLYSFQVIPVLGEVIAGD.KS
Retrocopy DIYTIAFGIQNVTHIGQATQEAHWVLKPGGWFLCLEFSQVNNPLISRLYDLYSFQVIPVLGEVIAGD*KS

Parental  YQ-YLVESIRRFPSQEEFKEMIEDAGFHKVTYESLTSGIVAIHSAFKL
          YQ..LVESI.RF.SQEEFKEMIE.AGFHKVTY.SLTSG..AIHSAFKL
Retrocopy YQ<TLVESIQRFLSQEEFKEMIEGAGFHKVTYDSLTSGMLAIHSAFKL

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	0.00 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_3050 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3050 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3050 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,