RetrogeneDB ID: retro_pabe_278

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:97799900..97800404(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GEMIN2
• Ensembl ID: ENSPPYG00000005764
• Aliases: None
• Description: gem (nuclear organelle) associated protein 2 [Source:HGNC Symbol;Acc:10884]

Sequence

>retro_pabe_278
AAGTTGAAAAGGAAGCAAGGTGTGAATGTTTCTCTTTTAGGATGCCAACCTGCCCCTGAAGGTTATTCCCCAATACTTCA
GTGGCAATAGCAAGTGGCACCGTTTTCAATGTAAGACAGAATGTGCACAAACATAGAAGTCACTGGAAATCACGACAGTT
GGATAGTAATGTGACTATGCCAAAATCTAAAGATGAAGAAGGCTGGAAGAAATTTTGTCTGAGTGAAAGTTTATATGCTG
GTGTGGTCACTGACAGCTACAAATGAAAGTCCTAGAACTGATTATGTACAAATTGGTTTTCCTCCCTTGGTTAGTATTGC
TAGCAGAATGAATCAGACAACAGTAGCTACTGTCTTGGAATATCTGAGTAATTGGTTTGGAGAAAGAGACTTTACTTTGG
ATTTGAGAAGATGGCTTTATGTCTTATTGGCTTGCCTTGAAAAACCTTTATTACATGAGGTTCATTCACTGATTCAGCAG
CTTGCAAGAAGGTGCTCTGAAGTG

Alignment

ORF - retro_pabe_278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.65 %
• Parental protein coverage: 60.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLKRKQSVNISLSGCQPAPEGYSPTLQWQQQQVAQFS-TVRQNVNKHRSHWKSQQLDSNVTMPKSEDEEG
          KLKRKQ.VN.SL.GCQPAPEGYSP.LQWQ.Q.VA.FS..VRQNV.KHRSHWKS.QLDSNVTMPKS.DEEG
Retrocopy KLKRKQGVNVSLLGCQPAPEGYSPILQWQ*Q-VAPFS<NVRQNVHKHRSHWKSRQLDSNVTMPKSKDEEG

Parental  WKKFCLGEKLCADGAVGPA-TNESPGIDYVQIGFPPLLSIVSRMNQATVTSVLEYLSNWFGERDFTPELG
          WKKFCL.E.L.A.G.V....TNESP..DYVQIGFPPL.SI.SRMNQ.TV..VLEYLSNWFGERDFT..L.
Retrocopy WKKFCLSESLYA-GVVTDS>TNESPRTDYVQIGFPPLVSIASRMNQTTVATVLEYLSNWFGERDFTLDLR

Parental  RWLYALLACLEKPLLPEAHSLIRQLARRCSEV
          RWLY.LLACLEKPLL.E.HSLI.QLARRCSEV
Retrocopy RWLYVLLACLEKPLLHEVHSLIQQLARRCSEV

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	4.15 RPM
SRP007412_cerebellum	0.00 RPM	6.32 RPM
SRP007412_heart	0.00 RPM	2.92 RPM
SRP007412_kidney	0.03 RPM	3.75 RPM
SRP007412_liver	0.03 RPM	3.27 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_278 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_278 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_278 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_455
Pan troglodytes	retro_ptro_342
Gorilla gorilla	retro_ggor_438

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016248	1 retrocopy	retro_cjac_2630,
Dasypus novemcinctus	ENSDNOG00000018278	1 retrocopy	retro_dnov_1040,
Homo sapiens	ENSG00000092208	1 retrocopy	retro_hsap_455,
Gorilla gorilla	ENSGGOG00000016691	2 retrocopies	retro_ggor_1844, retro_ggor_438,
Microcebus murinus	ENSMICG00000004811	1 retrocopy	retro_mmur_1221,
Myotis lucifugus	ENSMLUG00000002619	1 retrocopy	retro_mluc_1005,
Mus musculus	ENSMUSG00000060121	1 retrocopy	retro_mmus_354,
Pongo abelii	ENSPPYG00000005764	1 retrocopy	retro_pabe_278 ,
Pan troglodytes	ENSPTRG00000006291	1 retrocopy	retro_ptro_342,