RetrogeneDB ID: retro_ptro_2947

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: AACZ03168825.1:1409..1990(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HOOK3
• Ensembl ID: ENSPTRG00000020213
• Aliases: None
• Description: None

Sequence

>retro_ptro_2947
AAGCGAGTAATAGTGGAATGGCTAAGAGATCCATCTCAGGAGCCGAATTTATTGATAATATTCTTAATCAGGATGCAAAG
AATTATCATGCCTGGCAGCATCGACAATGGGTTATTCAGAAATTTAAACTTTGGGATAATGAGCTGCAATATGTGGACCA
ATTTCTCAAAGAGGATGTGAGAAATAACTCTGTCTGGAACCAAAGATATTTTGTTATTTCTAACACCACTGGCTACAATG
ATTGTGCTGTATTGGAGACAGAAGTCCAATACACTCTGGAAATGATTCAACTAGTACCACATAATAGTTCATGGAACTAT
TTGAAAGGAATTTTGCAGGATCGTGGTCTTTCCAAATATCCTAATCTGTTAAATCAATTACTTGATTTACAACCAAGTCA
TAGTTCCCCCTACCTAATTGCCTTTCTTGTGGGTATCTATGAAGACAAGCTAGAAAACCAGTGTGTCAATAAGGAAGACA
TTCTTAATAATGCATTAGGGTTATGTGAAATCCTAGCTAAAGAAAAGGACATGATAAGAAAAGAATATTGGAGATATATT
TGAAGATGCTTTCAAAGCAAA

Alignment

ORF - retro_ptro_2947 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.78 %
• Parental protein coverage: 50.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRVLVEWLRDPSQE-LEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQR
          .RV.VEWLRDPSQE..EFI..ILNQDAKNYHAWQHRQWVIQ.FKLWDNELQYVDQ.LKEDVRNNSVWNQR
Retrocopy KRVIVEWLRDPSQE<AEFIDNILNQDAKNYHAWQHRQWVIQKFKLWDNELQYVDQFLKEDVRNNSVWNQR

Parental  YFVISNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDLQPSHSSPY
          YFVISNTTGYND.AVLE.EVQYTLEMI.LVPHN.S.WNYLKGILQDRGLSKYPNLLNQLLDLQPSHSSPY
Retrocopy YFVISNTTGYNDCAVLETEVQYTLEMIQLVPHN-SSWNYLKGILQDRGLSKYPNLLNQLLDLQPSHSSPY

Parental  LIAFLVDIYEDMLENQCDNKEDILNKALELCEILAKEKDTIRKEYWRYIGRSLQSK
          LIAFLV.IYED.LENQC.NKEDILN.AL.LCEILAKEKD.IRKEYWRYI.R..QSK
Retrocopy LIAFLVGIYEDKLENQCVNKEDILNNALGLCEILAKEKDMIRKEYWRYI*RCFQSK

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	0.13 RPM	63.92 RPM
SRP007412_cerebellum	0.86 RPM	78.72 RPM
SRP007412_heart	1.40 RPM	56.89 RPM
SRP007412_kidney	0.86 RPM	67.13 RPM
SRP007412_liver	0.85 RPM	49.43 RPM
SRP007412_testis	0.74 RPM	71.77 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2947 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2947 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2947 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
Pan troglodytes	ENSPTRG00000020213	1 retrocopy	retro_ptro_2947 ,