RetrogeneDB ID: retro_ggor_2935

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:80087107..80088308(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG4A
• Ensembl ID: ENSGGOG00000002971
• Aliases: None
• Description: None

Sequence

>retro_ggor_2935
ATGGAGTCAGTTTTATCGAAGTATGAAAACCAGATTACTACTTTCACTGAATACCTCGAAGAATATTTAGATACAGATGA
GCTGGTATGGATCTTAGAAAAGCAGCATCTTATTAAAACAGAAACATCTAAGCTCTTGTCTGATATAAGTGTTTGTCTAT
AGTTTACATACAGAAGGAAATTTTCACCAATTTGGGGAACGGGCCCTTCATCAGATGCTGGTTGGGGATGTATGCCATGC
TGTGGACAGATGATGCTGGCTCAAGCCCTTATATGTAGACACTTGGGAAAGGACTGTTATTGGGAGATAACAAAAAGAAC
AACAACAACAACAATAAAATACCAATGGATCCTACAGTGCTTCTTAGAGAGAAAAAATTGTTGCTACACTATCCATCAAA
TGGCACAAATGGGTGTAGGAGACGGGAAATCAATTGGAGAATGGTTTGGACCAAATACAGTTGCACAGATGTTAATAAAA
AACTCGCTTTATTTGATGAATGGAATTCCTTGGCTCTTTGTGTTTCAATGGATAACAGTGGTCATTGAAGATATCAAAAA
ATGTGCTGTGTCCTTCCCTTGAGTGCTTACACAGACCGTGACAGGCCTCCTGATTCTCTGACTGCTTTAAACTAGAGTAA
GGGCACCTCCACCTACTGCCTAGCCTGGAAACCCCTGCTGCTTATTATGCCCCTTTGCCTGGGCATAAACCAAAACAACC
CTGTCTATGTTGATGCATTCAAACAGTATTTTAAGATGCCACAGTCTTTAGGGGCATTAGGAGAAAAACCAAATAATGCC
TATTATTTCAAAGAATTCTTAGTTGATAAGCTCATCTTCTTGGACCCTCACACAACCCAGACCTTTGTCAACACTGAAGA
GAATGAAACAGTTGATGACCAGACTTTCCATTGCCTGCAGTCCCCACAGCGAATGAACATACTGAACCTGGATCCTTCAG
TTGCATTGGGATTTTTCTGAAAATAAGAAAAAGACTTTAATAACTGGCATAGCCTTGTTCAGAAGGAAATTCTAAAGGAG
CATTTAAAGATGTTTGAATTGATTCGGAAACATCCATTGCACTGGCCTCGCCTTGTACCTCCAGCCAAGCCAGAAGTGAC
AACCACTGGGGCATAATTCATTGACTCTACTGAACAACTGGAGGAGTTTGATCTGGAGGAAATTTTGAGACTCTGAATGT
G

Alignment

ORF - retro_ggor_2935 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.15 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LEKVLSKYEDQITIFTDYLEEYPDTDELVWILGKQHLLKTEKSKLLSDISARLWFTYRRKFSPIGGTGPS
          .E.VLSKYE.QIT.FT.YLEEY.DTDELVWIL.KQHL.KTE.SKLLSDIS..L.FTYRRKFSPI.GTGPS
Retrocopy MESVLSKYENQITTFTEYLEEYLDTDELVWILEKQHLIKTETSKLLSDISVCL*FTYRRKFSPIWGTGPS

Parental  SDAGWGCMLRCGQMMLAQALICRHLGREDWSWEKQKEQPK---EYQRILQCFLDRKDCCYSIHQMVKTAQ
          SDAGWGCM..CGQMMLAQALICRHLG..D..WE..K........YQ.ILQCFL.RK.CCY.IHQM...AQ
Retrocopy SDAGWGCMPCCGQMMLAQALICRHLGK-DCYWEITKRTTTTTIKYQWILQCFLERKNCCYTIHQM---AQ

Parental  MGVGEGKSIGEWFGPNTVAQVLKKLALFDEWNSLAVYVSMDNTVVIEDIKK-MCRVLPLSADTAGDRPPD
          MGVG.GKSIGEWFGPNTVAQ.L.K..L..........V....TVVIEDIKK.MC.VLPLSA.T..DRPPD
Retrocopy MGVGDGKSIGEWFGPNTVAQMLIKNSLYLMNGIPWLFVFQWITVVIEDIKK<MCCVLPLSAYTDRDRPPD

Parental  SLTASNQSKGTSAYCSAWKPLLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKPNNAYYFIGFLG
          SLTA.N.SKGTS.YC.AWKPLLLI.PL.LGINQ.NPVYVDAFK..FKMPQSLGALG.KPNNAYYF..FL.
Retrocopy SLTALN*SKGTSTYCLAWKPLLLIMPLCLGINQNNPVYVDAFKQYFKMPQSLGALGEKPNNAYYFKEFLV

Parental  DELIFLDPHTTQTFVDTEENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEIL
          D.LIFLDPHTTQTFV.TEEN.TV.DQTFHCLQSPQRMNILNLDPSVALGFF.K.EKDF.NW.SLVQKEIL
Retrocopy DKLIFLDPHTTQTFVNTEENETVDDQTFHCLQSPQRMNILNLDPSVALGFF*K*EKDFNNWHSLVQKEIL

Parental  KENLRMFELVQKHPSHWPPFVPPAKPEVTTTGAEFIDSTEQLEEFDLEE-DFEILSV
          KE.L.MFEL..KHP.HWP..VPPAKPEVTTTGA.FIDSTEQLEEFDLEE..FE.L.V
Retrocopy KEHLKMFELIRKHPLHWPRLVPPAKPEVTTTGA*FIDSTEQLEEFDLEE<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	4.17 RPM
SRP007412_cerebellum	0.00 RPM	7.33 RPM
SRP007412_heart	0.00 RPM	4.78 RPM
SRP007412_kidney	0.00 RPM	14.52 RPM
SRP007412_liver	0.00 RPM	12.00 RPM
SRP007412_testis	0.00 RPM	4.25 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2935 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2935 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3139
Pongo abelii	retro_pabe_3666

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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,