RetrogeneDB ID: retro_nleu_996

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397278.1:24721540..24722302(+)
• Located in intron of: ENSNLEG00000010412

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAR1A
• Ensembl ID: ENSNLEG00000001982
• Aliases: None
• Description: None

Sequence

>retro_nleu_996
TCTTTAGCCAAAGCCATTGAAAAGAATGTGCTGATTTCACATCTTGATGATAATGAGAGAAGTGATATTTTTGATGCCAT
GTTTCCAGTCTCCTTTATCACTGGAGAGACAGTGATTCTGCAAGGTGATGAAGGGGATAACTTCTAGGTGATTGAGCAAG
GAGAGAGGGATGTCTGTGTCAGTGATGAATGAGCAACCAGTGTTGAAGAAGGAGGGAGCTTTGGAGAATTTGTTTTGATT
TATGGAACACCTAGAGTAGCCACTGTCAAAGCAAAGGCAAATGTGAAATGGTAGTGTATCAACCGAGACAGCTGTAGAAC
AATCCATATGGGAAGCACACTGAGAAAGTGGAAGATGTATGAGGAATTCCTTAGTAAAGTGTCTATTTTAGAGTCTCTGG
GTAAGTGAGAGCATCTTATGGTAGCTGATACATGGGAACCAGTCAAGTTTGAAGATTGGCAGAAGTTTGTGGTGCAGGGA
GAGCCAGGGGATGAGTTCCTTATTATTCTAGAGGGGCCAGCTGCTATGCTGCAACGTTGGTCAGACAATGAATAGTTTGT
TGAAGTGGGAAGATTGGGGCCTTCTGATTATTTTGGTGAATTTGCATTCCTGATGAATCACCCTCCTGCTGCCACGGTGG
TTGTACATGGCCCCTTGAAGTACATTAAGCTGGACCAGCCTAGATTTGAATGTGCTCTTGGCCCATGCTCAGACCTCCTC
AAACGAAACATCCAGCAGTACAACAGTTTTGTGTCACTGTCT

Alignment

ORF - retro_nleu_996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.53 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALAKAIEKNVLFSHLDDNERSDIFDAMFSVSFIAGETVIQQGDEGDNFYVIDQGETDVYVNNEWATSVGE
          .LAKAIEKNVL.SHLDDNERSDIFDAMF.VSFI.GETVI.QGDEGDNF.VI.QGE.DV.V..E.ATSV.E
Retrocopy SLAKAIEKNVLISHLDDNERSDIFDAMFPVSFITGETVILQGDEGDNF*VIEQGERDVCVSDE*ATSVEE

Parental  GGSFGELALIYGTPRAATVKAKTNVKLWGIDRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLT
          GGSFGE..LIYGTPR.ATVKAK.NVK...I.RDS.R.I.MGSTLRK.KMYEEFLSKVSILESL.K.E.L.
Retrocopy GGSFGEFVLIYGTPRVATVKAKANVKW*CINRDSCRTIHMGSTLRKWKMYEEFLSKVSILESLGK*EHLM

Parental  VADALEPVQFEDGQKIVVQGEPGDEFFIILEGSAAVLQRRSENEEFVEVGRLGPSDYFGEIALLMNRPRA
          VAD..EPV.FED.QK.VVQGEPGDEF.IILEG.AA.LQR.S.NE.FVEVGRLGPSDYFGE.A.LMN.P.A
Retrocopy VADTWEPVKFEDWQKFVVQGEPGDEFLIILEGPAAMLQRWSDNE*FVEVGRLGPSDYFGEFAFLMNHPPA

Parental  ATVVARGPLKCVKLDRPRFERVLGPCSDILKRNIQQYNSFVSLS
          ATVV..GPLK..KLD.PRFE..LGPCSD.LKRNIQQYNSFVSLS
Retrocopy ATVVVHGPLKYIKLDQPRFECALGPCSDLLKRNIQQYNSFVSLS

Legend:

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

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_996 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000108946	1 retrocopy	retro_hsap_186,
Gorilla gorilla	ENSGGOG00000016507	1 retrocopy	retro_ggor_267,
Macaca mulatta	ENSMMUG00000002194	2 retrocopies	retro_mmul_2498, retro_mmul_393,
Nomascus leucogenys	ENSNLEG00000001982	1 retrocopy	retro_nleu_996 ,
Pan troglodytes	ENSPTRG00000009579	1 retrocopy	retro_ptro_172,
Ictidomys tridecemlineatus	ENSSTOG00000012903	1 retrocopy	retro_itri_104,