RetrogeneDB ID: retro_sscr_210

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:299711523..299712228(-)
• Located in intron of: ENSSSCG00000005600

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAG1
• Ensembl ID: ENSSSCG00000000185
• Aliases: None
• Description: Sus scrofa protein kinase, AMP-activated, gamma 1 non-catalytic subunit (PRKAG1), mRNA. [Source:RefSeq mRNA;Acc:NM_001001642]

Sequence

>retro_sscr_210
CATGCTGACCATAAATCAGCCTTGGTACAGATTTATGAGCTTGAAGAATGCAAGACAGAAACTTGGAGAGAGATGTACCT
ACAGGACTCCTTTAAACCACTTTGTCTGCATTTCTCCTAATGCCAGCTTGTTTGATGCTGTCTCTATATTAACTCAAAAC
AAGATCCACAGGCTGCGAGTTATTGACCCAGAATCCGGCAACACCTTGTACATCCTCACCCACAAGAGCATCCTCAAGTT
CCTCAAGCTGTTTATCACTGAGTTCCCCAAGGTCGAGTTCATGTCTAAGTCTCCGGAAGAGCTACAGATTGGCACCTGTG
CCAACACTGCTATGGTCTGCACTACCACCCCCGTCTATGTGGCTCTGGGCGTCTTTGTACAGCACCGAGTCTCAGCCGTG
CCAGTGGTGGATGAAAAAGGGTATGTGGTGGCCATCTACTTCAAGTTTGACATTATCAACCTGGCAGCAGAAAAGACCTA
CAACAATCTAGAGGTATCTGTGACCAAAGCCCTGCAACATTGATCACATTACTTTGACGGTCTCCTCAAGTGCTACCTGC
ATGAGACCCTGAAAACCATCACCAATAGGCTGGTAAAAGCAGAGGTTCCCGACTTGTAGTGGCAGATGAGAATGACATGG
TCAAAGGAACTGTATCGTTGTCTGACATCCTGCAGGCCCTGGTGCTCACAAGAGGAGAGAAGCCC

Alignment

ORF - retro_sscr_210 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.81 %
• Parental protein coverage: 78.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HRYYKSALVQIYELEEHKIETWREVYLQDSFKPL-VCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTL
          H...KSALVQIYELEE.K.ETWRE.YLQDSFKPL.VCISPNASLFDAVS.L..NKIHRL.VIDPESGNTL
Retrocopy HADHKSALVQIYELEECKTETWREMYLQDSFKPL>VCISPNASLFDAVSILTQNKIHRLRVIDPESGNTL

Parental  YILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQHRVSALPVVDEK
          YILTHK.ILKFLKLFITEFPK.EFMSKS.EELQIGT.AN.AMV.TTTPVYVALG.FVQHRVSA.PVVDEK
Retrocopy YILTHKSILKFLKLFITEFPKVEFMSKSPEELQIGTCANTAMVCTTTPVYVALGVFVQHRVSAVPVVDEK

Parental  GRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHRSHYFEGVLKCYLHETLETIINRLVEAEV-HRLVVV
          G.VV.IY.KFD.INLAAEKTYNNL.VSVTKALQH.SHYF.G.LKCYLHETL.TI.NRLV.AEV..RLVV.
Retrocopy GYVVAIYFKFDIINLAAEKTYNNLEVSVTKALQH*SHYFDGLLKCYLHETLKTITNRLVKAEV<SRLVVA

Parental  DENDVVKGIVSLSDILQALVLTGGEKP
          DEND.VKG.VSLSDILQALVLT.GEKP
Retrocopy DENDMVKGTVSLSDILQALVLTRGEKP

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
SRP014902_placenta	0.00 RPM	26.94 RPM
SRP014902_testis	0.28 RPM	44.56 RPM
SRP018288_heart	0.05 RPM	47.25 RPM
SRP018288_kidney	0.10 RPM	35.76 RPM
SRP018288_liver	0.00 RPM	26.70 RPM
SRP018288_lung	0.10 RPM	47.04 RPM
SRP018856_adipose	0.00 RPM	93.67 RPM
SRP035408_brain	0.00 RPM	49.32 RPM
SRP035408_liver	0.00 RPM	33.96 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_210 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_210 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_210 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,