RetrogeneDB ID: retro_ocun_829

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:40155165..40156054(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAG1
• Ensembl ID: ENSOCUG00000008409
• Aliases: None
• Description: protein kinase, AMP-activated, gamma 1 non-catalytic subunit [Source:HGNC Symbol;Acc:9385]

Sequence

>retro_ocun_829
GTCACTTCTTCAGATAGGTGCCCAGTCTTGGAAAATGAGCATACTTAAGACACCCCAGAATGCAACAATTGCATGTACAC
TCACTTCATGGAGTCTCATCGCTGCTATGACCTGATCCTCCAAAGCTCCAAACTCGTTGTATTTGACACTTCCCTACAAG
TGAAGAAGGCTTTCTTTGTGTGGATGACTGATCGTGTGCCAGCTCCACTTTGTAGGAAAGTAAGAAGAAAAGTAGTGGGC
AAGCTGATTGTTGCTGACTTCATCAATATCTTGCACTGCTGCTATAAATCAACCTTGTTACAAATCTATGAGCTAGAAGA
ACCTAAGAGAGAAACTTGGAGAGAAGTGTACCTACAAGATTCCTTCAAACCACTTGTCTGTATTTCTCCTAATGCCAGCT
TGTTTGATGCTCTCTCTTCATTAATTCTAAACAAGACCCACAGACTGCCAGTTATTGGCCTGGAAATAGGCAACACCTTG
TTTGTCCTCATCCACAAGTGCATCCTCAAATTTATCTCTGACCTCCTCAAGCTGCAATTCATGTCCAAATCTCTGGAAGA
GCTACAGAATAGCACATATACCAATATTGCTATGGTCTACACAAACACCCCCATCTTTGTGGCTCTGGGCATCTGTGTCC
AGTATTGAGTTTCAGCCCTGCCAGTGGTGGATGAGAAAGGGCTTGTGGGTCACATCTACTCCAAATTTGAAGTTAGCATT
CTGGCAGCAGCAAAGATCTACAATAACCAGATGAGTCTGTGACTAAAGCCCTGCAGCCTTGGTCACAGTACCGTGAGGCT
GTCCTCAAGCACTACCTGTGTGAGATTCTGGAGGCCATCATCAACAGACTGGCAGAAGCAGAGTTCACTGACTTGCAGTG
GTGGACCAG

Alignment

ORF - retro_ocun_829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.43 %
• Parental protein coverage: 91.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VTASDSCSAVKNEHSQDTPDSNNSVYTSFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAP
          VT.SD.C....NEH..DTP..NN..YT.FM.SHRCYDLI..SSKLVVFDTSLQVKKAFF...T..V..AP
Retrocopy VTSSDRCPVLENEHT*DTPECNNCMYTHFMESHRCYDLILQSSKLVVFDTSLQVKKAFFVWMTDRV-PAP

Parental  LWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVS
          L........VG.L...DFINILH..YKS.L.QIYELEE.K.ETWREVYLQDSFKPLVCISPNASLFDA.S
Retrocopy LCRKVRRKVVGKLIVADFINILHCCYKSTLLQIYELEEPKRETWREVYLQDSFKPLVCISPNASLFDALS

Parental  SLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMTKSLQELQIGTYANIAMVRTTTPV
          SLI.NK.HRLPVI..E.GNTL..L.HK.ILKF.........K..FM.KSL.ELQ..TY.NIAMV.T.TP.
Retrocopy SLILNKTHRLPVIGLEIGNTLFVLIHKCILKFI----SDLLKLQFMSKSLEELQNSTYTNIAMVYTNTPI

Parental  YVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNL-DVSVTKALQHRSHYFEGVLKCYLH
          .VALGI.VQ..VSALPVVDEKG.V..IYSKF.V..LAA.K.YNN..D.SVTKALQ..S.Y.E.VLK.YL.
Retrocopy FVALGICVQY*VSALPVVDEKGLVGHIYSKFEVSILAAAKIYNNQ<DESVTKALQPWSQYREAVLKHYLC

Parental  ETLETIINRLVEAE-VHRLVVVDE
          E.LE.IINRL.EAE.VH.L.VVD.
Retrocopy EILEAIINRLAEAE<VH*LAVVDQ

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
SRP017611_brain	0.11 RPM	31.62 RPM
SRP017611_kidney	0.00 RPM	32.13 RPM
SRP017611_liver	0.00 RPM	21.27 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_829 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_829 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,