RetrogeneDB ID: retro_ggor_2873

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:89364282..89364957(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APIP
• Ensembl ID: ENSGGOG00000022940
• Aliases: None
• Description: None

Sequence

>retro_ggor_2873
GCGCAGGACAAGGAGCATCCAAGATACCTGATCCCAGAACTTTGCAAACAGTTTTACCACTTGGGCTGGGTCACTGGGAC
TGGAGGAGGAATTAGCTTAAGGCATGGCGATGAAATCTACATTACTCCTTCAGGAGTGCAAAAGGAACGAATTCAGCCTG
AAGACATGTTTGTTTGTGATATAAATGAAAAGGACATAAGTGGACCTTCGCCATCTAAGAAGCTAAAATAAAGCCAGTAT
ACTCCTCTTCTCATGAATGCTTACACAATGAGAGGAGCAGGTGCGGTGATTCATACCCACTGTAAAGCTGCTTTGATGGC
CACCCTTCTCTTTCCAGGACGGGAGTTTAAAATTACACATCAAGAGATGATAAAAGGAATAAAGAAATGTACTTCCGGAG
GGTATTATAGATATGATGATATGTTAGTGGCACCCATTATTGAGAATACACCTGAGGAGAAAGACCTCAAAGATAGAATG
GCTCATGCAATGAATGAATACCCAGACTCCTGTGCAGTACTGGTCAGACGTCATGGAGTATATGTGTGGGGGGAAACATG
GGAGAAGGCCAAAACCATGTGTGAGTGTTATGACTATTTATTTGATATTGCCGTATCAATGAAGAAAGTAGGACTTGATC
CTTCACAGCTCCCAGTTGGAGAAAATGGAATTGTG

Alignment

ORF - retro_ggor_2873 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.56 %
• Parental protein coverage: 86.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQDKEHPRYLIPELCKQFYHLGWVTGTGGGISLKHGDEIYIAPSGVQKERIQPEDMFVCDINEKDISGPS
          .QDKEHPRYLIPELCKQFYHLGWVTGTGGGISL.HGDEIYI.PSGVQKERIQPEDMFVCDINEKDISGPS
Retrocopy AQDKEHPRYLIPELCKQFYHLGWVTGTGGGISLRHGDEIYITPSGVQKERIQPEDMFVCDINEKDISGPS

Parental  PSKKLKKSQCTPLFMNAYTMRGAGAVIHTHSKAAVMATLLFPGREFKITHQEMIKGIKKCTSRGYYRYDD
          PSKKLK.SQ.TPL.MNAYTMRGAGAVIHTH.KAA.MATLLFPGREFKITHQEMIKGIKKCTS.GYYRYDD
Retrocopy PSKKLK*SQYTPLLMNAYTMRGAGAVIHTHCKAALMATLLFPGREFKITHQEMIKGIKKCTSGGYYRYDD

Parental  MLVVPIIENTPEEKDLKDRMAHAMNEYPDSCAVLVRRHGVYVWGETWEKAKTMCECYDYLFDIAVSMKKV
          MLV.PIIENTPEEKDLKDRMAHAMNEYPDSCAVLVRRHGVYVWGETWEKAKTMCECYDYLFDIAVSMKKV
Retrocopy MLVAPIIENTPEEKDLKDRMAHAMNEYPDSCAVLVRRHGVYVWGETWEKAKTMCECYDYLFDIAVSMKKV

Parental  GLDPSQLPVGENGIV
          GLDPSQLPVGENGIV
Retrocopy GLDPSQLPVGENGIV

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	7.19 RPM
SRP007412_cerebellum	0.00 RPM	6.11 RPM
SRP007412_heart	0.00 RPM	3.94 RPM
SRP007412_kidney	0.00 RPM	22.20 RPM
SRP007412_liver	0.00 RPM	13.19 RPM
SRP007412_testis	0.00 RPM	19.89 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_2873 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2873 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000016758	1 retrocopy	retro_etel_220,
Homo sapiens	ENSG00000149089	1 retrocopy	retro_hsap_4208,
Gorilla gorilla	ENSGGOG00000022940	2 retrocopies	retro_ggor_2818, retro_ggor_2873 ,
Ornithorhynchus anatinus	ENSOANG00000007394	6 retrocopies	retro_oana_108, retro_oana_109, retro_oana_121, retro_oana_63, retro_oana_85, retro_oana_96,
Pongo abelii	ENSPPYG00000003361	1 retrocopy	retro_pabe_3442,
Pan troglodytes	ENSPTRG00000003499	1 retrocopy	retro_ptro_2856,
Sarcophilus harrisii	ENSSHAG00000011523	1 retrocopy	retro_shar_574,
Ictidomys tridecemlineatus	ENSSTOG00000004390	1 retrocopy	retro_itri_1029,