RetrogeneDB ID: retro_pabe_1390

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:36524310..36524874(-)
• Located in intron of: ENSPPYG00000007334

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000018534
• Aliases: None
• Description: None

Sequence

>retro_pabe_1390
TGTCACTGGACACATTCAGAACCAGTATCAATGACAGACTTGGATATACAATATACTTACCTTGGGGGTCATGTATGTTT
ATCTGCACATGCAAGAAATGGTTCAAAACAATGGGGGACCTATGCAGAAGCTATAACCGCATGTGGTCAACACAGGTTAT
GTAGATTCCAAGGATGCAGATATCTTAGTGACATAAATATAACAAGATATAACATAAATTGCATAGAGAATGGGGTTTGC
AATGAACTTTTCTATTCTCAGTGTGATCCTGGTTATGCTCCTCCAGATTGTGAGCTGGCAATATCATCACCAGGAGGAAG
TGTTAATAATGGATTTTGGCTTACGGTAGAAAAAAGTGTACCCTTGTTTCCAAAATGACGTGCTGCTCCTAAAGACAATG
GTCTTTTGATCAGTTTCTACATTTCTTTTTTACCTTTGCTCATTTTAATTGCTTTTGTTGGTCTTAAATGGAATAAAATG
AAGAGATTTTGGAGCAAAGCGGGAACAGTAAGCAGCAGATCTATCTCAGAAGACAGCAGTAGGAACAACAACCAGTCACA
GAGT

Alignment

ORF - retro_pabe_1390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.19 %
• Parental protein coverage: 79.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CHWIHSELVPMTDLDIQYTYLGGHVCLSAHARNRSKQSETYTEDITACGQHKACRSQECRNFSELNITKC
          CHW.HSE.V.MTDLDIQYTYLGGHVCLSAHARN.SKQ..TY.E.ITACGQH..CR.Q.CR..S..NIT..
Retrocopy CHWTHSEPVSMTDLDIQYTYLGGHVCLSAHARNGSKQWGTYAEAITACGQHRLCRFQGCRYLSDINITRY

Parental  TTNCGQNGICNEHFHCQCDPGYAPPDCEPAMSSPGGSIDDGFWLTIEKSVPLFPKRRAAPKNNGLLISFY
          ..NC..NG.CNE.F..QCDPGYAPPDCE.A.SSPGGS...GFWLT.EKSVPLFPK.RAAPK.NGLLISFY
Retrocopy NINCIENGVCNELFYSQCDPGYAPPDCELAISSPGGSVNNGFWLTVEKSVPLFPK*RAAPKDNGLLISFY

Parental  I-FSPLLILIAIVSLKWNKMKRFWSKVGTVSSRSISEDSSSNNSQSQS
          I.F.PLLILIA.V.LKWNKMKRFWSK.GTVSSRSISEDSS.NN.QSQS
Retrocopy ISFLPLLILIAFVGLKWNKMKRFWSKAGTVSSRSISEDSSRNNNQSQS

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1390 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1390 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1390 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000018534	1 retrocopy	retro_pabe_1390 ,