RetrogeneDB ID: retro_ptro_869

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:55667110..55667832(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNF4G
• Ensembl ID: ENSPTRG00000020357
• Aliases: None
• Description: hepatocyte nuclear factor 4, gamma [Source:HGNC Symbol;Acc:5026]

Sequence

>retro_ptro_869
ACTTCTGCCCCAGAGAGGACAAATATGAATACCCAGACAACAGTCTCATCTGTCTTTGTGCTATATGTGAGTCAAGGCAA
CAGGAAAACACTGTGGGGCATCGAGCTGTGGTGGGTGCAAGGGCTTCTTCAGATGCAGCATATGCAAGAGTAACGTTTAT
TCTTGCAGGTTCCGTCGGCAATGTTTTGTTGACAAGGCCAAAAGAAATCAATGTAGATACTGTCAATTAAGAAAGTGTTT
TAGAGCAGGAATGGAAAAAGAAGTTGTGCATAATGAATGCAATAGAACAAGCACCAGAAGAAGCACATGTGATGGCAGCA
ATATCCCCTCCATTAACACACTGGCACAAGCTGAAGTTCTGTCTTGCCAGATCTCAGTCTCAAGCCTTGGGGCAAGTACT
GATATACATGTTAAAAAAATAAAAAATAAAGGTGTTGGTGATGTCTGTGAATTTCTGAAACAGCAGCTCTTAGTCTTGGT
GGAATGGGCTAAATATATTCCTGCCTTCTGTCAGTTACCATTGGATGGTAAGGTGGCACTGTTGAGATCTCATGCAGGAG
GACACTTAACTGCCTGGAGCTATAAAGAGATCCATGATGTATAAAGATATTTTGCTTTTGGGAAACAACTATATTATTCA
CTGCAACAGCTGTGAATTTGAGATTAGCAGTGTAATCAGTCGGGTTCTAGATGAGCTGGTTCAACCATTTCAAGAAATCC
AA

Alignment

ORF - retro_ptro_869 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.64 %
• Parental protein coverage: 53.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSAPE-TSMNTT-DNGVNCLCAICGDR-ATGKHYGASSCDGCKGFFRRSIRKSHVYSCRFSRQCVVDKDK
          .SAPE.T.MNT..DN...CLCAIC..R.ATGKH.GASSC.GCKGFFR.SI.KS.VYSCRF.RQC.VDK.K
Retrocopy TSAPERTNMNTQ<DNSLICLCAICESR<ATGKHCGASSCGGCKGFFRCSICKSNVYSCRFRRQCFVDKAK

Parental  RNQCRYCRLRKCFRAGMKKEAVQNERDRISTRRSTFDGSNIPSINTLAQAEVRSRQISVSSPGSSTDINV
          RNQCRYC.LRKCFRAGM.KE.V.NE..R.STRRST.DGSNIPSINTLAQAEV.S.QISVSS.G.STDI.V
Retrocopy RNQCRYCQLRKCFRAGMEKEVVHNECNRTSTRRSTCDGSNIPSINTLAQAEVLSCQISVSSLGASTDIHV

Parental  --KKIASIGDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHL-LLGATKRSMMYKDILLL
          ........GDVCE..KQQLLVLVEWAKYIPAFC.LPLD..VALLR.HAG.HL.L.GA.KRSMMYKDILLL
Retrocopy XXXXXXGVGDVCEFLKQQLLVLVEWAKYIPAFCQLPLDGKVALLRSHAGGHL>LPGAIKRSMMYKDILLL

Parental  GNNYVIHRNSCEVEISRVANRVLDELVRPFQEIQ
          GNNY.IH.NSCE.EIS.V..RVLDELV.PFQEIQ
Retrocopy GNNYIIHCNSCEFEISSVISRVLDELVQPFQEIQ

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	0.04 RPM
SRP007412_cerebellum	0.00 RPM	0.18 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	14.54 RPM
SRP007412_liver	0.00 RPM	2.62 RPM
SRP007412_testis	0.00 RPM	7.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_869 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_869 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_869 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000938	1 retrocopy	retro_chof_1831,
Pan troglodytes	ENSPTRG00000010661	1 retrocopy	retro_ptro_1242,
Pan troglodytes	ENSPTRG00000020357	1 retrocopy	retro_ptro_869 ,