RetrogeneDB ID: retro_pabe_489

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:204518378..204518621(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPF
• Ensembl ID: ENSPPYG00000004847
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide F [Source:HGNC Symbol;Acc:11162]

Sequence

>retro_pabe_489
GTAAGTCTACCCCTCAATCCCGAAGCTTTCCTCAGTGGGTTAACAGGAAAGCCGGTGATGCTGAAACGAAGTGGGGAATG
GAGTACAAGGGCTGTCTGGAATCTTAGATGGCTACATGAACATGCAGCTTGCAAATAAGAGAAATACATAGGTAGGGAGC
TGTCTAGACATCTGGGTGAAGTTTTAATACGGTATAAAAATATCCTTTATAGTAGAGGTATGGAAGAAAAGGAAGAAAAT
GGG

Alignment

ORF - retro_pabe_489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.59 %
• Parental protein coverage: 95.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSLPLNPKPFLNGLTGKPVMVK-LKWGMEYKGYLVS-VDGYMNMQLANT-EEYIDGALSGHLGEVLIRCN
          .SLPLNP..FL.GLTGKPVM.K..KWGMEYKG.L.S..DGYMNMQLAN..E.YI...LS.HLGEVLIR..
Retrocopy VSLPLNPEAFLSGLTGKPVMLK<TKWGMEYKGCLES<LDGYMNMQLANK<EKYIGRELSRHLGEVLIRYK

Parental  NVLYIRGVEEEEEDG
          N.LY.RG.EE.EE.G
Retrocopy NILYSRGMEEKEENG

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	0.11 RPM	6.75 RPM
SRP007412_cerebellum	0.00 RPM	9.73 RPM
SRP007412_heart	0.00 RPM	7.89 RPM
SRP007412_kidney	0.00 RPM	11.34 RPM
SRP007412_liver	0.00 RPM	9.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_489 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_489 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_489 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_125
Gorilla gorilla	retro_ggor_225
Macaca mulatta	retro_mmul_361

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002166	3 retrocopies	retro_amel_1239, retro_amel_42, retro_amel_883,
Bos taurus	ENSBTAG00000016271	1 retrocopy	retro_btau_765,
Equus caballus	ENSECAG00000019817	1 retrocopy	retro_ecab_154,
Felis catus	ENSFCAG00000029966	4 retrocopies	retro_fcat_280, retro_fcat_66, retro_fcat_77, retro_fcat_861,
Homo sapiens	ENSG00000139343	3 retrocopies	retro_hsap_125, retro_hsap_2487, retro_hsap_2645,
Gorilla gorilla	ENSGGOG00000001127	2 retrocopies	retro_ggor_1549, retro_ggor_225,
Macaca mulatta	ENSMMUG00000009302	4 retrocopies	retro_mmul_1521, retro_mmul_361, retro_mmul_550, retro_mmul_893,
Mustela putorius furo	ENSMPUG00000007176	3 retrocopies	retro_mputfur_1309, retro_mputfur_377, retro_mputfur_941,
Mus musculus	ENSMUSG00000020018	4 retrocopies	retro_mmus_1060, retro_mmus_1197, retro_mmus_2537, retro_mmus_3210,
Nomascus leucogenys	ENSNLEG00000005835	3 retrocopies	retro_nleu_2259, retro_nleu_274, retro_nleu_651,
Pongo abelii	ENSPPYG00000004847	2 retrocopies	retro_pabe_381, retro_pabe_489 ,
Pongo abelii	ENSPPYG00000015105	1 retrocopy	retro_pabe_1994,
Pteropus vampyrus	ENSPVAG00000009036	1 retrocopy	retro_pvam_1170,
Rattus norvegicus	ENSRNOG00000005556	4 retrocopies	retro_rnor_1822, retro_rnor_1849, retro_rnor_2926, retro_rnor_444,
Sus scrofa	ENSSSCG00000000895	1 retrocopy	retro_sscr_958,