RetrogeneDB ID: retro_cjac_3045

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:9883851..9884597(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAG1
• Ensembl ID: ENSCJAG00000020827
• Aliases: None
• Description: None

Sequence

>retro_cjac_3045
GTGGGTATGCTGACCATCACTGATTTCATCAATATTCTGCACCGCTACTATAAATCAGCCTTGGTACAGATCTATGGGCT
AGAAGAACACAAGATGGAAATTGGAGAGAGGTGTACCTCCAGGACTCCTTTAAACCGCTTGTCTGCATTTCTCCTAATGC
CAGCTTGTTCGATGCTGTCTCTTCATTAATTCGGAACAAGATCCACAGGCTGCCAGTTATTGACCCAGAATCGGGCAATA
CTTTGTACATCCTCACCCACAAGCGCATTCTGAAGTTCCTCAAATTGTTTATCACTGAATTTCCCAAGCCAGAGTTCATG
TCCAAGTCTCTGGAAGAGCTACAGATTGGCACCTATGCCAATATTGCTATGGTTCGCACTACTACCCCCGTCTGTGTGGC
TCTGGGCATTTTTGTACAGCATTGAGTCTCAGCTCTGCCAGTGGTGGATGAGAAGGGGCGTGTGGTGGACATCTACTCCA
AGTTTGATGTGATCAATCTGGCAGCAGAAAAGACCTACAACAACCTAGACGTGTCTGTGACTGAAGCCCTGCAACGTCGG
TCACACTACTTTGAGGGTGTTCTCAAGTGCTACCTGCATGAGACTCTGGAGACCATCATCGACAGGCTAGTGGAAGCAGA
GGTTCACCGACTTGTAGTGGTGGATGAAAATGATGTGGTCAAGGGAATTGTATCACTGTCTGACATCCTGCAGGCCCTGG
TGCTCACAGGTGGAGAGAAGAATCCC

Alignment

ORF - retro_cjac_3045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96. %
• Parental protein coverage: 73.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGMLTITDFINILHRYYKSALVQIYELEEHKIE-TWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIH
          .GMLTITDFINILHRYYKSALVQIY.LEEHK.E..WREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIH
Retrocopy VGMLTITDFINILHRYYKSALVQIYGLEEHKME<NWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIH

Parental  RLPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFV
          RLPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPV.VALGIFV
Retrocopy RLPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVCVALGIFV

Parental  QHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHRSHYFEGVLKCYLHETLETIINR
          QH.VSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVT.ALQ.RSHYFEGVLKCYLHETLETII.R
Retrocopy QH*VSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTEALQRRSHYFEGVLKCYLHETLETIIDR

Parental  LVEAEVHRLVVVDENDVVKGIVSLSDILQALVLTGGEKNP
          LVEAEVHRLVVVDENDVVKGIVSLSDILQALVLTGGEKNP
Retrocopy LVEAEVHRLVVVDENDVVKGIVSLSDILQALVLTGGEKNP

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	0.02 RPM	11.16 RPM
SRP051959_heart	0.05 RPM	16.80 RPM
SRP051959_kidney	0.07 RPM	12.62 RPM
SRP051959_liver	0.02 RPM	11.65 RPM
SRP051959_lung	0.02 RPM	8.02 RPM
SRP051959_lymph_node	0.00 RPM	7.17 RPM
SRP051959_skeletal_muscle	0.02 RPM	9.32 RPM
SRP051959_spleen	0.00 RPM	8.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3045 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3045 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3045 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006964	2 retrocopies	retro_amel_1722, retro_amel_406,
Choloepus hoffmanni	ENSCHOG00000006397	1 retrocopy	retro_chof_32,
Callithrix jacchus	ENSCJAG00000020827	2 retrocopies	retro_cjac_3045 , retro_cjac_3892,
Felis catus	ENSFCAG00000000091	1 retrocopy	retro_fcat_1730,
Myotis lucifugus	ENSMLUG00000011156	2 retrocopies	retro_mluc_2417, retro_mluc_451,
Oryctolagus cuniculus	ENSOCUG00000008409	1 retrocopy	retro_ocun_829,
Sus scrofa	ENSSSCG00000000185	1 retrocopy	retro_sscr_210,
Tursiops truncatus	ENSTTRG00000004730	1 retrocopy	retro_ttru_497,