RetrogeneDB ID: retro_ptro_2856

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:106011077..106011803(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039793
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: APIP
• Ensembl ID: ENSPTRG00000003499
• Aliases: None
• Description: Methylthioribulose-1-phosphate dehydratase [Source:UniProtKB/TrEMBL;Acc:H2Q3E7]

Sequence

>retro_ptro_2856
ATGTCTGGCTGTGACGCCCAGGAGGGAGACTGTTGTTCCCCGAGATGCGGAGCGCAGGACAAGGAGCATCCAAGATACCT
GATCCCAGAACTTTGCAAACAGTTTTACCATTTGCGCTGGGTCACTGGGACTGGAGGAGGAATTAGCTTGAGGCATGGCG
GTGAAATCTACATTGCTCCTTCAGAAGTGCAAAAGGAACGAATTCAGCCTGAAGACATGTTTGTTTGTGATATAAATGAA
AAGGACATAAGTGGACCTTCGCCATCTAAGAAGCTAAAATAAAGCCAGTGTACTCCTCTTCTCATGAATGCTTACACAAT
GAGAGGAGCAGGTGCGGTGATTCATACCCACTCTAAAGCTGCTGTGATGGCCACCCTTCTCTTTCCAGGATGGGAGTTTA
AAATTACACATCAAGAGATGATCAAAGGAATAAAGAAATGTACTTCTGGAGGGTGTTATAGATATGATGATATGTTAGTG
GCACCCATTATTGAGAATACACCTGAGGAGAAAGACCTCAAAGATAGAATGGCTCATGCAATGAATGAATACCCAGACTC
CTGTGCAGTACTGGTCAGACGTCATGGAGTATATGTGTGGGGGGAAACATGGGAGAAGGCCAAAACCATGTGTGAGTGTT
ATGACTATTTATTTGATATTGCCGTATCAATGAAGAAAGTAGGACTTGATCCTTCACAGCTCCCAGTTGGAGAAAATGGA
ATTGTC

Alignment

ORF - retro_ptro_2856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGCDAREGDCCSRRCGAQDKEHPRYLIPELCKQFYHLGWVTGTGGGISLKHGDEIYIAPSGVQKERIQP
          MSGCDA.EGDCCS.RCGAQDKEHPRYLIPELCKQFYHL.WVTGTGGGISL.HG.EIYIAPS.VQKERIQP
Retrocopy MSGCDAQEGDCCSPRCGAQDKEHPRYLIPELCKQFYHLRWVTGTGGGISLRHGGEIYIAPSEVQKERIQP

Parental  EDMFVCDINEKDISGPSPSKKLKKSQCTPLFMNAYTMRGAGAVIHTHSKAAVMATLLFPGREFKITHQEM
          EDMFVCDINEKDISGPSPSKKLK.SQCTPL.MNAYTMRGAGAVIHTHSKAAVMATLLFPG.EFKITHQEM
Retrocopy EDMFVCDINEKDISGPSPSKKLK*SQCTPLLMNAYTMRGAGAVIHTHSKAAVMATLLFPGWEFKITHQEM

Parental  IKGIKKCTSGGYYRYDDMLVVPIIENTPEEKDLKDRMAHAMNEYPDSCAVLVRRHGVYVWGETWEKAKTM
          IKGIKKCTSGG.YRYDDMLV.PIIENTPEEKDLKDRMAHAMNEYPDSCAVLVRRHGVYVWGETWEKAKTM
Retrocopy IKGIKKCTSGGCYRYDDMLVAPIIENTPEEKDLKDRMAHAMNEYPDSCAVLVRRHGVYVWGETWEKAKTM

Parental  CECYDYLFDIAVSMKKVGLDPSQLPVGENGIV
          CECYDYLFDIAVSMKKVGLDPSQLPVGENGIV
Retrocopy CECYDYLFDIAVSMKKVGLDPSQLPVGENGIV

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	0.05 RPM	5.18 RPM
SRP007412_cerebellum	0.00 RPM	5.59 RPM
SRP007412_heart	0.03 RPM	8.98 RPM
SRP007412_kidney	0.05 RPM	10.75 RPM
SRP007412_liver	0.03 RPM	8.84 RPM
SRP007412_testis	0.00 RPM	9.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2856 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2856 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2856 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4208
Gorilla gorilla	retro_ggor_2818
Pongo abelii	retro_pabe_3442

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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,