RetrogeneDB ID: retro_ttru_497

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2484:633750..634408(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAG1
• Ensembl ID: ENSTTRG00000004730
• Aliases: None
• Description: protein kinase, AMP-activated, gamma 1 non-catalytic subunit [Source:HGNC Symbol;Acc:9385]

Sequence

>retro_ttru_497
AAGGTTCCTAAAGTGAATGAACCCAGCCAGTGCCTCTTGCAATGGAGATGGCCACGTCTTGAGAGTTTCCAACTCTGGAA
AAATGAGCGTCCTCAAGAGATCCCAGAATCTAACAACAGCGTATACACTTCCTTTATAGAGTCCCTTGCTGCTATGACTT
GATTCTCACAAGCTCCAATTTGGTTGTAGTTGCTACTTCCCTGCAGGTGAAGAAAGCTTTCTTTGCTTTGGTGACTAATG
GTATACAAGCTGCCCCTTTCTGGGACAGCAAAAAGCAAGGACTTGTGGGCGTGTGGACTACCACTGATTTCATCAATATC
CTGCACCGTTACTATAAATCAGCCTTGGTACAGATCTATGAGTTGGAAGAACACAAGACAGAAACTTGGAAGGAGGTGTA
CATACAGGACTTCTTTAAACCACTTGCCTGCATTTCTCCTAATGCCAGCATGTTTGATGCTGTCTCTTCATTAATTCAAA
ACAAGATCCACAGGCTGCCAGTTGTTAACCCAGAATCAGGCAACATCTTGTACATCCTCATCCACAAATGCAGTCTCAAG
TTCCTCAAATTGCTTATCACTAAGTTCCCAAGCCAGAGTTCACGTCTAAGTCTCTGGAAGAGCTACAAATCAGCTTCTAT
GCCAACACTGTTATGATG

Alignment

ORF - retro_ttru_497 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.52 %
• Parental protein coverage: 61.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLPKANEPSASVAMEAVTSSDNYSALENEHPQETPESNNSVYTSFMKSHR-CYDLIPTSSKLVVFDTSLQ
          K.PK.NEPS..................NE.PQE.PESNNSVYTSF..S...CYDLI.TSS.LVV..TSLQ
Retrocopy KVPKVNEPSQCLLQWRWPRLESFQLWKNERPQEIPESNNSVYTSFIESLA<CYDLILTSSNLVVVATSLQ

Parental  VKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYLQDSF
          VKKAFFALVTNG..AAP.WDSKKQ..VG..T.TDFINILHRYYKSALVQIYELEEHK.ETW.EVY.QD.F
Retrocopy VKKAFFALVTNGIQAAPFWDSKKQGLVGVWTTTDFINILHRYYKSALVQIYELEEHKTETWKEVYIQDFF

Parental  KPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITEF-PKPEFMSKSLEE
          KPL.CISPNAS.FDAVSSLI.NKIHRLPV..PESGN.LYIL.HK..LKFLKL.IT.F.PKPEF.SKSLEE
Retrocopy KPLACISPNASMFDAVSSLIQNKIHRLPVVNPESGNILYILIHKCSLKFLKLLITKF<PKPEFTSKSLEE

Parental  LQIGTYANIAMV
          LQI..YAN..M.
Retrocopy LQISFYANTVMM

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_497 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_497 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 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 ,