RetrogeneDB ID: retro_ptro_3139

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:82870785..82871516(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG4A
• Ensembl ID: ENSPTRG00000022170
• Aliases: None
• Description: Pan troglodytes autophagy related 4A, cysteine peptidase (ATG4A), mRNA. [Source:RefSeq mRNA;Acc:NM_001246528]

Sequence

>retro_ptro_3139
GTTAATAAAAAACTCGCTTTATTTGATGAATGGAATTCCTTGGCTCTTTATGTTTCAATGGATAACAGTGGTCATTGAAG
ATATCAAAAAATGTGCTGTGTCCTTCCCTTGAGTGCTGACACAGACCGTGACAGGCCTCCTGATTCTCTGACTGCTTTAA
ACTAGAGTAAGGGCACCTCCACCTACTGCCTAGCCTGGAAACCCCTGCTGCTTATTATGCCCCTTTGCCTGGGCATAAAC
CAAAACAACCCTGTCTATGTTGATGCATTCAAACAGTATTTTAAGATGCCACAGTCTTTAGGGTCATTAGGAGAAAAACC
AAATAATGCCTATTGTTTCAAAGAATTCTTAGGTGATAAGCTCATCTTCTTGGACCCTCACACAACCCAGACCTTTGTCA
ACACTAAAGAGAATGAAACAGTTGATGATCAGACTTTCCATTGCCTGCAGTCCCCACAGCGAATGAACATACTGAACCTG
GATCCTTCAGTTGCATTGGGATTTTTCTGAAAATAAGAAAAAGACTTTAATAACTGGCATAGCCTTGTTCAGAAGGAAAT
TCTAAAGGAGCATTTAAAGATGTTTGAATTGATTCGGAAACATCCATTGCACTGGCCTCGCCTTGTACCTCCAGCCAAGC
CAGAAGTGACAACCACTGGGGCATAATTCATTGACTCTAGTGAACAACTGGAGGAGTTTGATCTGGAGGAAATTTTGAGA
CTCTGAATGTG

Alignment

ORF - retro_ptro_3139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.27 %
• Parental protein coverage: 61.56 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLKKLALFDEWNSLAVYVSMDNTVVIEDIKKMCRVLPLSIDTPGDRPPDSLTASNQSKGTSAYCSAWKPL
          V.KKLALFDEWNSLA.YVSMDN.......K..C.VLPLS.DT..DRPPDSLTA.N.SKGTS.YC.AWKPL
Retrocopy VNKKLALFDEWNSLALYVSMDNSGH*RYQKMCC-VLPLSADTDRDRPPDSLTALN*SKGTSTYCLAWKPL

Parental  LLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTTQTFVDTEENG
          LLI.PL.LGINQ.NPVYVDAFK..FKMPQSLG.LG.KPNNAY.F..FLGD.LIFLDPHTTQTFV.T.EN.
Retrocopy LLIMPLCLGINQNNPVYVDAFKQYFKMPQSLGSLGEKPNNAYCFKEFLGDKLIFLDPHTTQTFVNTKENE

Parental  TVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQKHPSHWPPFV
          TV.DQTFHCLQSPQRMNILNLDPSVALGFF.K.EKDF.NW.SLVQKEILKE.L.MFEL..KHP.HWP..V
Retrocopy TVDDQTFHCLQSPQRMNILNLDPSVALGFF*K*EKDFNNWHSLVQKEILKEHLKMFELIRKHPLHWPRLV

Parental  PPAKPEVTTTGAEFIDSTEQLEEFDLEE-DFEILSV
          PPAKPEVTTTGA.FIDS.EQLEEFDLEE..FE.L.V
Retrocopy PPAKPEVTTTGA*FIDSSEQLEEFDLEE<NFETLNV

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	4.72 RPM
SRP007412_cerebellum	0.00 RPM	5.74 RPM
SRP007412_heart	0.00 RPM	12.42 RPM
SRP007412_kidney	0.00 RPM	12.87 RPM
SRP007412_liver	0.00 RPM	9.43 RPM
SRP007412_testis	0.00 RPM	4.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3139 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3139 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2935
Pongo abelii	retro_pabe_3666

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000002971	1 retrocopy	retro_ggor_2935,
Mus musculus	ENSMUSG00000079418	1 retrocopy	retro_mmus_2283,
Nomascus leucogenys	ENSNLEG00000014016	1 retrocopy	retro_nleu_1993,
Pongo abelii	ENSPPYG00000020619	1 retrocopy	retro_pabe_3666,
Pan troglodytes	ENSPTRG00000022170	1 retrocopy	retro_ptro_3139 ,