RetrogeneDB ID: retro_cjac_3892

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285907.1:58861..59608(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000011613
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_3892
GTGGGTCTGCTGACCATCACTGATTTCATCAATATTCTGCACCGCTACTATAAATCAGCCTTGGTACAGATCTATGAGCT
AGAAGAACACAAGATAAAAACTTGGAGAGAGGTGTACCTCCAGGACTCCTTTAAACCGCTTGTCTGCATTTCTCCTAATG
CCAGCTTGCTTGATGCTGTCTCTTCATTAATTCGGAACAAGATCCACAGGCTGCCAGTTATTGACCCAGAATCGGGCAAT
ACTTTGCACATCCTCACCCACAAACGCATTCTGAAGTTCCTCAAATTGTTTATCACTGAATTTCCCAAGCCAGAGTTCAT
GTCCAAGTCTCTGGAAGAGCTACAGATTGGCACCTATGCCAATATTGCTATGGTTCGCACTACTACCCCCGTCTATGTGG
CTCTGGGCATTTTTGTACAGCATCGAGTCTCAGCTCTGCCAGTGGTGGATGAGAAGGGGCGTGTGGTGGACATCTACTCC
AAGTTTGATGTGACCAATCTGGCAGCAGAAAAGACCTACAACAACCTAGACGTGTCTGTGACTGAAGCCCTGCAACATCG
ATCACACTACTTTGAGGGTGTTCTCAAGTGCCACCTGCATGAGACTCTGGAGACCATCATCAACAGGCTAGAGGAAGCAG
AGGTTCACCGACTTGTAGTGGTGGATGAAAATGATGTGGTCAAGGGAATTGTATCACGGTCTGACATCCTGCAGGCCCTG
GTGCTCACAGGTGGAGAGAAGAATCCC

Alignment

ORF - retro_cjac_3892 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.98 %
• Parental protein coverage: 73.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIHR
          .G.LTITDFINILHRYYKSALVQIYELEEHKI.TWREVYLQDSFKPLVCISPNASL.DAVSSLIRNKIHR
Retrocopy VGLLTITDFINILHRYYKSALVQIYELEEHKIKTWREVYLQDSFKPLVCISPNASLLDAVSSLIRNKIHR

Parental  LPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQ
          LPVIDPESGNTL.ILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQ
Retrocopy LPVIDPESGNTLHILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQ

Parental  HRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHRSHYFEGVLKCYLHETLETIINRL
          HRVSALPVVDEKGRVVDIYSKFDV.NLAAEKTYNNLDVSVT.ALQHRSHYFEGVLKC.LHETLETIINRL
Retrocopy HRVSALPVVDEKGRVVDIYSKFDVTNLAAEKTYNNLDVSVTEALQHRSHYFEGVLKCHLHETLETIINRL

Parental  VEAEVHRLVVVDENDVVKGIVSLSDILQALVLTGGEKNP
          .EAEVHRLVVVDENDVVKGIVS.SDILQALVLTGGEKNP
Retrocopy EEAEVHRLVVVDENDVVKGIVSRSDILQALVLTGGEKNP

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	0.38 RPM	11.16 RPM
SRP051959_heart	0.51 RPM	16.80 RPM
SRP051959_kidney	0.29 RPM	12.62 RPM
SRP051959_liver	0.11 RPM	11.65 RPM
SRP051959_lung	1.19 RPM	8.02 RPM
SRP051959_lymph_node	0.73 RPM	7.17 RPM
SRP051959_skeletal_muscle	0.11 RPM	9.32 RPM
SRP051959_spleen	0.46 RPM	8.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3892 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3892 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3892 has 0 orthologous retrocopies within eutheria group .

---

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,