RetrogeneDB ID: retro_pabe_3442

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:103433957..103434683(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APIP
• Ensembl ID: ENSPPYG00000003361
• Aliases: None
• Description: APAF1 interacting protein [Source:HGNC Symbol;Acc:17581]

Sequence

>retro_pabe_3442
ATGTCTGGCTATGACGCTCGGGAGGGAGACTGTTGTTCCCGGAGATGCGGAGCACAGGACAAGGAGCACCCAAGACACCT
GATCCCAGAACTTTGCAAACAGTTTTACCATTTGGGCTAGGTCACTGGGACTGGAGGAGGAATTAGCTTGAAGCATGGCG
ATGAAATCTACATTGCTCCTTCAGGAGTGCAAAAGGAGCGAATTCAGCCTGAAGACATGTTTGTTTGTGATATAATTGAA
AAGGACATAAGTGGACCTTCGCCATCTAAGAAGCTAAAAAAAAGCCAGTGTACTCCTCTTTTCACAAATGCTTACACAAT
GAGAGGAGCAGGTGCAGTGATTCATACCCACTCTAAAGCTGCTGTGATGGCCACCCTTCTCTTTCCAGGATGGGATTTTA
AAATTACACATCAGGAAATGATAAAAGGAATAAAGAAATGTACTTCCGGAGGGTATTATAGATATGATGATATGTTAGTG
GTACCCATTATTGAGAATACACCTGAGGAGAAAGACCTCAAAGATAGAATGGCTCACGCAATGAATGAATACCCAGACTC
CTGTGCAGTACTGGTCAGATGTCATGCAGTATATATGTGGGGGGAAACATGGGAGAAGGCCAAAACCCTGTGTGAGTGTT
ATGACTATTTATTTGATATTGCCGTATCAATGAAGAAAGTAGGACTTGATCCTTCACAGCTCCCAGTTGGAGAAAATGTA
ATTGTC

Alignment

ORF - retro_pabe_3442 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.56 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGCDAREGDCCSWRCGAQDKEHPRYLIPELCKQFYHLGWVSGTGGGISLKHGDEIYIAPSGVQKERIQP
          MSG.DAREGDCCS.RCGAQDKEHPR.LIPELCKQFYHLG.V.GTGGGISLKHGDEIYIAPSGVQKERIQP
Retrocopy MSGYDAREGDCCSRRCGAQDKEHPRHLIPELCKQFYHLG*VTGTGGGISLKHGDEIYIAPSGVQKERIQP

Parental  EDMFVCDINEKDISGPSPSKKLKKSQCTPLFMNAYTMRGAGAVIHTHSKAAVMATLLFPGREFKITHQEM
          EDMFVCDI.EKDISGPSPSKK....QCTPLF.NAYTMRGAGAVIHTHSKAAVMATLLFPG..FKITHQEM
Retrocopy EDMFVCDIIEKDISGPSPSKKXXXXQCTPLFTNAYTMRGAGAVIHTHSKAAVMATLLFPGWDFKITHQEM

Parental  IKGIKKCTSGGYYRYDDMLVVPIIENTPEEKDLKDRMAHAMNEYPDSCAVLVRRHGVYVWGETWEKAKTM
          IKGIKKCTSGGYYRYDDMLVVPIIENTPEEKDLKDRMAHAMNEYPDSCAVLVR.H.VY.WGETWEKAKT.
Retrocopy IKGIKKCTSGGYYRYDDMLVVPIIENTPEEKDLKDRMAHAMNEYPDSCAVLVRCHAVYMWGETWEKAKTL

Parental  CECYDYLFDIAVSMKKVGLDPSQLPVGENGIV
          CECYDYLFDIAVSMKKVGLDPSQLPVGEN.IV
Retrocopy CECYDYLFDIAVSMKKVGLDPSQLPVGENVIV

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	0.06 RPM	5.31 RPM
SRP007412_cerebellum	0.00 RPM	6.08 RPM
SRP007412_heart	0.00 RPM	4.97 RPM
SRP007412_kidney	0.07 RPM	13.09 RPM
SRP007412_liver	0.00 RPM	8.97 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3442 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3442 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3442 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4208
Pan troglodytes	retro_ptro_2856
Gorilla gorilla	retro_ggor_2818

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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,