RetrogeneDB ID: retro_pabe_138

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1_random:333098..333629(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000010598
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000015218
• Aliases: None
• Description: None

Sequence

>retro_pabe_138
ATGAACACGGTGCTGTCGCGAGCGAACTCGCTGTTTGCCTTCTCGCTGAGCGTGATGCCGGCGCTCACCTTCGGCTGCTT
CATCACCACCGCCTTCAAAGACAGGAGCGTCCCGGTGCGGCTGCACGTCTCGCTGATCAAGCTAAAAAGTGTAGGTTTCA
CTGGACCTAGAGAAAGAAGTGATCTGGGATTTATCACATTGGATATAACTGCTGATCTAGAGAGTATATTTGATTGGAAT
GTTAAGCAGTTGTTTCTTTATTTATCAGCAGAATATTCAACAAAAAATAATACTCTGAACCAAGTTGTCCTATGGGACAA
GATTGTTTTGAGAGGTGATAATCCGAAGCTGCTGCTGAAAGATATGAAAACAAAATATTTTTTCTTTGACGATGGAAATG
GTCTCAAGGGAAACAGGAATGTCACTCTGACCCTGTCTTGGAACGTCGTACCAAATGCTGGAATTCTACCTCTTGTGACA
GGATCAGGACACGTATCTGTCCCATTTCCAGATACATACGAAATAACGAAG

Alignment

ORF - retro_pabe_138 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.38 %
• Parental protein coverage: 98.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNTVLSRANSLFAFSLSVMAALTFGCFITTAFKDRSVPVRLHVSRIMLKNVEDFTG-RERSDLGFITFDI
          MNTVLSRANSLFAFSLSVM.ALTFGCFITTAFKDRSVPVRLHVS.I.LK.V..FTG.RERSDLGFIT.DI
Retrocopy MNTVLSRANSLFAFSLSVMPALTFGCFITTAFKDRSVPVRLHVSLIKLKSV-GFTGPRERSDLGFITLDI

Parental  TADLENIFDWNVKQLFLYLSAEYSTKNNALNQVVLWDKIVLRGDNPKLLLKDMKTKYFFFDDGNGLKGNR
          TADLE.IFDWNVKQLFLYLSAEYSTKNN.LNQVVLWDKIVLRGDNPKLLLKDMKTKYFFFDDGNGLKGNR
Retrocopy TADLESIFDWNVKQLFLYLSAEYSTKNNTLNQVVLWDKIVLRGDNPKLLLKDMKTKYFFFDDGNGLKGNR

Parental  NVTLTLSWNVVPNAGILPLVTGSGHVSVPFPDTYEITK
          NVTLTLSWNVVPNAGILPLVTGSGHVSVPFPDTYEITK
Retrocopy NVTLTLSWNVVPNAGILPLVTGSGHVSVPFPDTYEITK

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	6.47 RPM
SRP007412_cerebellum	0.12 RPM	5.84 RPM
SRP007412_heart	0.00 RPM	9.57 RPM
SRP007412_kidney	0.03 RPM	11.30 RPM
SRP007412_liver	0.03 RPM	22.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_138 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_138 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_138 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000001987	2 retrocopies	retro_mmur_1595, retro_mmur_731,
Oryctolagus cuniculus	ENSOCUG00000029741	1 retrocopy	retro_ocun_119,
Otolemur garnettii	ENSOGAG00000003825	1 retrocopy	retro_ogar_1710,
Pongo abelii	ENSPPYG00000015218	1 retrocopy	retro_pabe_138 ,
Sarcophilus harrisii	ENSSHAG00000015012	1 retrocopy	retro_shar_481,
Ictidomys tridecemlineatus	ENSSTOG00000013678	1 retrocopy	retro_itri_57,