RetrogeneDB ID: retro_amel_406

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192428.1:2926952..2927528(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAG1
• Ensembl ID: ENSAMEG00000006964
• Aliases: None
• Description: protein kinase, AMP-activated, gamma 1 non-catalytic subunit [Source:HGNC Symbol;Acc:9385]

Sequence

>retro_amel_406
GTCCCTTCTTCAGACAGCTCCCCAGGCTCTGGAAAATGAGCATCCTCAAGAGATCTCAGAATCCAACAACAGGGTGTAAA
CTTCCTTCTTGAAGTTTCATCGCTGGGGTGACCAGATTCCCACGAGCTCCAAACTGGTTGTATTTGATACTTCCCTGCAG
GTGCAGAAAGCTGTCTTTGCTTTGGTGGCTAATGGTGTATGAGCTGTCCCTTTGTTGGATAGTAAAAAGCCGAGTTTTGT
AGGCATGCTGGCCATCACCAGCTTCATCCATATCGTGCATTGCTACTGTAACTCAGCCTTGGTAGGGATCTAGGAGCTGG
AAGAACACAAGGTAGAAAGTTGGACAGAGGTGTACCTACAGGACTCCTTCGCACCACTCGCCTGCATTTCTCCTAATGCC
AGCTTGTTTGGTGCTGTGTCCTCATTAATTTTGAAAACAGATCCACAGGCTGCCAGTTACTGACCCGGAATCAGGCAACA
CCTTGTTCATCCTCCCCCACAGGCGCATCCTCAAGTTCCTCCAATGTTTTATCACGGTTTCCCGAGCCGGAGTTCCTGTC
TGAGTCTCTGAAGGAG

Alignment

ORF - retro_amel_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.49 %
• Parental protein coverage: 58.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VTSSDSSP-ALENEHPQETPESNNSVYTSFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAA
          V.SSDSSP.ALENEHPQE..ESNN.V.TSF.K.HR..D.IPTSSKLVVFDTSLQV.KA.FALV.NGV.A.
Retrocopy VPSSDSSP>ALENEHPQEISESNNRV*TSFLKFHRWGDQIPTSSKLVVFDTSLQVQKAVFALVANGV*AV

Parental  PLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAV
          PL.DSKK.SFVGML.IT.FI.I.H.Y..SALV.I.ELEEHK.E.W.EVYLQDSF.PL.CISPNASLF.AV
Retrocopy PLLDSKKPSFVGMLAITSFIHIVHCYCNSALVGI*ELEEHKVESWTEVYLQDSFAPLACISPNASLFGAV

Parental  SSLIR-NKIHRLPVIDPESGNTLYILTHKRILKFLKLFIT-EFP-KPEFMSKSLEE
          SSLI....IHRLPV.DPESGNTL.IL.H.RILKFL..FIT..FP..PEF.S.SL.E
Retrocopy SSLIL>KQIHRLPVTDPESGNTLFILPHRRILKFLQCFIT<GFP<EPEFLSESLKE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_406 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_406 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006964	2 retrocopies	retro_amel_1722, retro_amel_406 ,
Ailuropoda melanoleuca	ENSAMEG00000013406	1 retrocopy	retro_amel_1890,
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,