RetrogeneDB ID: retro_pabe_3384

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:23085026..23086010(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARMC8
• Ensembl ID: ENSPPYG00000014140
• Aliases: None
• Description: armadillo repeat-containing protein 8 [Source:RefSeq peptide;Acc:NP_001126485]

Sequence

>retro_pabe_3384
GTATTAAAGACATTGTCTTATTTGGTTCAAATGTGCAGTACAAAGAGATTACTAGAGGAGAGAGTTAAAGGAGCTGAGAC
ACTTGCCTATCTGATTGAACCAGATATTGAGCTACAGAGAATCGCTAGTGTAACTGATCACCTCATTGCCATGCTTGCTG
ACTATTTCAAGTATCCCAACTCATTGAGTGCCATCACTGATGTTAAAAGGCTTGATCATGTTTTAAAACATGCTCATGAA
CTCTGCCAGGCTGCATTTAATCTCTACGACTCTCTTAGAGCAAATGATGAAGACATTCAGAAGAAAAGCCCTGAGACTGA
AAATATGATGGACTGAATTGTGATGGCTTGTCTGAGTCTAGTGTCAAGGTGCGGTTTCCTGCTGTCAGATGTTTGCACCG
TTTATCCAGATCTGTGCAGCAGCTTCAAAACAGTTTCTAGGATCACACTCTGTGAAAACCTTTAATGAAGGTTTTACAAA
ATGCACCAGATGAAATCCTAGTAGTAGCATCTTCCATGGTATATAATCTTCTTGAATTTTCTCCAAGGAAAGAGTCAATT
TTAAAATCAGGAGTTGTAAAGCTACTTTGTGGATTAACCCAGAGTGAAAATCCTGCTTTACGAGTGAGCAGAATTTGGGC
TTTAATGAATATGGCATTTCAGGCTGAACAAAAAATAAAAGCAGACATGTTACAAAGCTTGAGTACTGAACAGCTATTCT
GGTTATTATCAGATTCAGATTTGAATGTGCTGATGAAGACACTGGGACTTCTTAGAAATCTCCTCTTGACCTGGCTTCAT
ATAATAAAATAATGAGTACTCATGGAAAGCAAATTATGCAAGCTGTCATCCTTATTCTGGAAGGGGAACATAACTTTAAG
GTCAAAGAGTAGATACTGTGCATCTTAGCCAATATAGAAGATGAGACAACAGCAAAGAATGTATTATGACCAATGATGAT
ATCCTTCAGAAAATCAAATATTAC

Alignment

ORF - retro_pabe_3384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.98 %
• Parental protein coverage: 55.46 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLKTLPCLVRMCSKERLLEERVEGAETLAYLIEPDVELQRIASITDHLIAMLADYFKYPSSVSAITDIKR
          VLKTL..LV.MCS..RLLEERV.GAETLAYLIEPD.ELQRIAS.TDHLIAMLADYFKYP.S.SAITD.KR
Retrocopy VLKTLSYLVQMCSTKRLLEERVKGAETLAYLIEPDIELQRIASVTDHLIAMLADYFKYPNSLSAITDVKR

Parental  LDHDLKHAHELRQAAFKLYASLGANDEDIRKKIIETENMMDRIV-TGLSESSVKVRLAAVRCLHSLSRSV
          LDH.LKHAHEL.QAAF.LY.SL.ANDEDI.KK..ETENMMD.IV..GLSESSVKVR..AVRCLH.LSRSV
Retrocopy LDHVLKHAHELCQAAFNLYDSLRANDEDIQKKSPETENMMD*IV<DGLSESSVKVRFPAVRCLHRLSRSV

Parental  QQLRTSFQDHAVWKPLMKVLQNAPDEILVVASSMLCNLLLEFSPSKEPILESGAVELLCGLTQSENPALR
          QQL..SF.DH...KPLMKVLQNAPDEILVVASSM..N.LLEFSP.KE.IL.SG.V.LLCGLTQSENPALR
Retrocopy QQLQNSF*DHTL*KPLMKVLQNAPDEILVVASSMVYN-LLEFSPRKESILKSGVVKLLCGLTQSENPALR

Parental  VNGIWALMNMAFQAEQKIKADILRSLSTEQLFRLLSDSDLNVLMKTLGLLRNLLSTRPHI-DKIMSTHGK
          V..IWALMNMAFQAEQKIKAD.L.SLSTEQLF.LLSDSDLNVLMKTLGLLRNLL.T..HI..KIMSTHGK
Retrocopy VSRIWALMNMAFQAEQKIKADMLQSLSTEQLFWLLSDSDLNVLMKTLGLLRNLLLTWLHI<NKIMSTHGK

Parental  QIMQAVTLILEGEHNIEVKEQTLCILANIADGTTAKDL-IMTNDDILQKIKNY
          QIMQAV.LILEGEHN..VKE..LCILANI.D.TTAK...IMTNDDILQKIK.Y
Retrocopy QIMQAVILILEGEHNFKVKE*ILCILANIEDETTAKNV<IMTNDDILQKIKYY

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	25.82 RPM
SRP007412_cerebellum	0.00 RPM	45.60 RPM
SRP007412_heart	0.00 RPM	6.71 RPM
SRP007412_kidney	0.00 RPM	9.65 RPM
SRP007412_liver	0.00 RPM	7.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3384 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3384 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3384 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000114098	1 retrocopy	retro_hsap_4253,
Gorilla gorilla	ENSGGOG00000023535	1 retrocopy	retro_ggor_2851,
Macaca mulatta	ENSMMUG00000021285	1 retrocopy	retro_mmul_1142,
Pongo abelii	ENSPPYG00000014140	2 retrocopies	retro_pabe_3384 , retro_pabe_3385,