RetrogeneDB ID: retro_pabe_3666

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:81163479..81164224(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG4A
• Ensembl ID: ENSPPYG00000020619
• Aliases: ATG4A, APG4A
• Description: cysteine protease ATG4A [Source:RefSeq peptide;Acc:NP_001126588]

Sequence

>retro_pabe_3666
ACTTGCACAGATGTTAACAAAAAACTCACTTTATTTGATGAATGGAATTCCTTGGCTCTTTATGTTTCAATGGATAACAC
AGTGGTCATTGAAGATATCAAAAAATGTGCTGTGTCCTTCCCTTGAGTGCTTACACAGACCGTGACAGGCCTCCCGATTC
TCTGACTGCTTTAAACTAGAGTAAGGGCACCTCTACCTACTGCCTAGCCTGGATACCCCTGCTGCTTAATGTGCCCCTTT
GCCTGGGCATAAACCAAAACAACCCTGTCTATGTTGACGCATTCAAAGAGTGTTTTAAGATGCCACAGTCTTTAAGGGCA
TTAGAAGAAAAACAAATAATGCCTATTGTTTCAAAGAATTCTTAGGTGATAAGCTCATCTTCTTGGACCCTCACACAACC
CAGACCTTTGTCAACACTGAAGAGAATGAAATGGTTGATGATCAGACTTTCCATTGCCTGCAGTCCCCACAGAGAGTGAA
CATACTGAACCTAGATCCTTCAGTTGCATTGGGATTTTTCTGAAAATAAGAAAAAGACTTTAATAACTAGCATAGCCTTG
TTCAGAAGGAAATTCTAAAGGAGCATTTAAAGATGTTTGAATCGATTCAGAAACATCCATTGCACTGGCCTCACCTTGTA
CTTCCAGCCAAGCCAGAAGTGACAACCACTGGGGCATAATTCATTGACTCTACTGAACAACTGGAGGAGTTTGATATGGA
GGAAGATTTTGAGATTCTGAATGTG

Alignment

ORF - retro_pabe_3666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.48 %
• Parental protein coverage: 62.56 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TVAQVLKKLALFDEWNSLAVYVSMDNTVVIEDIKK-MCRVLPLSADTAGDRPPDSLTASNLSKGTSAYCS
          T...V.KKL.LFDEWNSLA.YVSMDNTVVIEDIKK.MC.VLPLSA.T..DRPPDSLTA.N.SKGTS.YC.
Retrocopy TCTDVNKKLTLFDEWNSLALYVSMDNTVVIEDIKK<MCCVLPLSAYTDRDRPPDSLTALN*SKGTSTYCL

Parental  AWKPLLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKP-NNAYYFIGFLGDELIFLDPHTTQTFV
          AW.PLLL.VPL.LGINQ.NPVYVDAFKECFKMPQSL.AL..K..NNAY.F..FLGD.LIFLDPHTTQTFV
Retrocopy AWIPLLLNVPLCLGINQNNPVYVDAFKECFKMPQSLRALEEKQ<NNAYCFKEFLGDKLIFLDPHTTQTFV

Parental  DTEENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQKHPS
          .TEEN..V.DQTFHCLQSPQR.NILNLDPSVALGFF.K.EKDF.N..SLVQKEILKE.L.MFE..QKHP.
Retrocopy NTEENEMVDDQTFHCLQSPQRVNILNLDPSVALGFF*K*EKDFNN*HSLVQKEILKEHLKMFESIQKHPL

Parental  HWPPFVPPAKPEVTTTGAEFIDSTEQLEEFDLEEDFEILSV
          HWP..V.PAKPEVTTTGA.FIDSTEQLEEFD.EEDFEIL.V
Retrocopy HWPHLVLPAKPEVTTTGA*FIDSTEQLEEFDMEEDFEILNV

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	5.53 RPM
SRP007412_cerebellum	0.00 RPM	9.97 RPM
SRP007412_heart	0.00 RPM	7.80 RPM
SRP007412_kidney	0.00 RPM	11.67 RPM
SRP007412_liver	0.00 RPM	11.23 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3666 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3666 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3666 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3139
Gorilla gorilla	retro_ggor_2935

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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,