RetrogeneDB ID: retro_pabe_265

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:80770613..80771288(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000005651
• Aliases: None
• Description: None

Sequence

>retro_pabe_265
AAGGCATGGAAGGAAGTTTGACTGCATAAGACAACATGGTTTAGGTCTGGGATATTACCTGGAGTTATTCAAGAGTTGCT
TGTGGACTACTGTGTGAAGATACAAGACACAAATTTAACTTCTGAGGACAAAAAGTTTCTTGAGACCCTTGAACAGTGGC
TACTCATAACTGAACTGACATGGCTCTTAGGTCCTAGCCAGGAGAGGGAGATACCTTCACTGCTAGAGCTGGAGAAAGCG
GACCTTCTGGAATACATGCCACTCTCAGAGGATTTTGTGTGGATGAGGGCTCTGCTACAGCAAGAAGTGGAGGAGTAGCT
CAAGAAGAAATGTTTCACTCTGCTCTGGTACTATGATCCCAATTCAGATGCTGACAGTGAAACCGTGAAGGCAGCAAACG
TGTGGAAACTTGCAGAGGTACTAGTGGGTAGGAAGCAGCAGTGCCAGGATGCCAAGAGCCAGCAAAAGGATCACGTGGTG
CTGCTGGAGAAGAAGAGTGCCACCTACTTCCAGGTGCTTCTCTGCTGTCTCACTTTGCTGCAGAGGCTTCTTCAGGAACA
ACGGCTGAAGACTCACTCCGAGTTAGACCACATCAATGCCCAGTACCTGGAAGTCAGGTGTGGTGCTATGGTACTTAAGC
TGAGGATGGAAGAGTTAAAGATTTTGTCCAACACA

Alignment

ORF - retro_pabe_265 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.0 %
• Parental protein coverage: 51.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAWKEVRLHKTTWLRSEILHRVIQELLVDYYVKIQDTNVTSEDKKFHETLEQRLLVTELMRLLGPSQERE
          .AWKEV.LHKTTW.RS.IL..VIQELLVDY.VKIQDTN.TSEDKKF.ETLEQ.LL.TEL..LLGPSQERE
Retrocopy KAWKEV*LHKTTWFRSGILPGVIQELLVDYCVKIQDTNLTSEDKKFLETLEQWLLITELTWLLGPSQERE

Parental  IPPLLGLEKADLLELMPLSEDFVWMRARLQQEVEEQLKKKCFSLLCYYDPNSDADSETVKAAKVWKLTEV
          IP.LL.LEKADLLE.MPLSEDFVWMRA.LQQEVEE.LKKKCF.LL.YYDPNSDADSETVKAA.VWKL.EV
Retrocopy IPSLLELEKADLLEYMPLSEDFVWMRALLQQEVEE*LKKKCFTLLWYYDPNSDADSETVKAANVWKLAEV

Parental  LVGEQQQCQDAKSQQKEQMLLLEKKSATYSQVLLRCLTLLQRLLQEHRLKTQSELDRINAQYLEVKCGAM
          LVG..QQCQDAKSQQK....LLEKKSATY.QVLL.CLTLLQRLLQE.RLKT.SELD.INAQYLEV.CGAM
Retrocopy LVGRKQQCQDAKSQQKDHVVLLEKKSATYFQVLLCCLTLLQRLLQEQRLKTHSELDHINAQYLEVRCGAM

Parental  ILKLRMEELKILSDT
          .LKLRMEELKILS.T
Retrocopy VLKLRMEELKILSNT

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	0.17 RPM	6.91 RPM
SRP007412_cerebellum	0.00 RPM	16.05 RPM
SRP007412_heart	0.51 RPM	2.77 RPM
SRP007412_kidney	0.20 RPM	23.07 RPM
SRP007412_liver	0.12 RPM	16.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_265 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_265 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_265 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_469
Pan troglodytes	retro_ptro_352
Gorilla gorilla	retro_ggor_447

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008389	1 retrocopy	retro_cjac_757,
Dasypus novemcinctus	ENSDNOG00000002575	1 retrocopy	retro_dnov_712,
Homo sapiens	ENSG00000092036	1 retrocopy	retro_hsap_469,
Gorilla gorilla	ENSGGOG00000007504	1 retrocopy	retro_ggor_447,
Myotis lucifugus	ENSMLUG00000012934	1 retrocopy	retro_mluc_1946,
Otolemur garnettii	ENSOGAG00000000586	1 retrocopy	retro_ogar_382,
Pongo abelii	ENSPPYG00000005651	1 retrocopy	retro_pabe_265 ,
Pan troglodytes	ENSPTRG00000006153	1 retrocopy	retro_ptro_352,