RetrogeneDB ID: retro_pabe_254

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:71618316..71618673(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD1
• Ensembl ID: ENSPPYG00000025874
• Aliases: None
• Description: small nuclear ribonucleoprotein D1 polypeptide 16kDa [Source:HGNC Symbol;Acc:11158]

Sequence

>retro_pabe_254
ATGAAGCTCGTGAGATTTTTGATGAAATTGAGTCATGAAACTGTAACCATTGAATTGAAGAATGGAACACAGGTCGATGG
AACAATCACAGGTGTGGATGTCAGCATGAATACACATCTTAAAGCTGTGAAAATGACCCTGAAGAACAGAGAACCTGTTT
AGCTGGAAACGCTGAGTATTCGAGGAAATAACATTCGGTATTTTATTCTACCAGACAGTTTACCTCTGGATACACTACTT
GTGGATGTTGAACCTAAGGTGAAATCTAAGAAAAGGGAAGCTGTTGCAGGAAGAGGCAGAGGCAGAGGAAGAAGAAGAGG
ACGTGGCCATGGCAGAGGAAAAGGGGGTCCCAGGCGA

Alignment

ORF - retro_pabe_254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFIL
          MKLVRFLMKLSHETVTIELKNGTQV.GTITGVDVSMNTHLKAVKMTLKNREPV.LETLSIRGNNIRYFIL
Retrocopy MKLVRFLMKLSHETVTIELKNGTQVDGTITGVDVSMNTHLKAVKMTLKNREPV*LETLSIRGNNIRYFIL

Parental  PDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR
          PDSLPLDTLLVDVEPKVKSKKREAV............RG.GRG.GGPRR
Retrocopy PDSLPLDTLLVDVEPKVKSKKREAVXXXXXXXXXXXXRGHGRGKGGPRR

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	19.02 RPM
SRP007412_cerebellum	0.00 RPM	23.71 RPM
SRP007412_heart	0.00 RPM	8.01 RPM
SRP007412_kidney	0.03 RPM	14.78 RPM
SRP007412_liver	0.00 RPM	10.74 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_254 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_254 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_254 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006364	1 retrocopy	retro_acar_129,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144, retro_btau_706, retro_btau_84,
Canis familiaris	ENSCAFG00000018247	1 retrocopy	retro_cfam_373,
Dasypus novemcinctus	ENSDNOG00000018773	4 retrocopies	retro_dnov_1254, retro_dnov_1716, retro_dnov_1832, retro_dnov_2403,
Felis catus	ENSFCAG00000012352	1 retrocopy	retro_fcat_1885,
Macaca mulatta	ENSMMUG00000003992	2 retrocopies	retro_mmul_887, retro_mmul_891,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Pongo abelii	ENSPPYG00000025874	3 retrocopies	retro_pabe_254 , retro_pabe_948, retro_pabe_952,
Pan troglodytes	ENSPTRG00000009909	2 retrocopies	retro_ptro_291, retro_ptro_781,
Pteropus vampyrus	ENSPVAG00000005511	1 retrocopy	retro_pvam_450,
Rattus norvegicus	ENSRNOG00000013714	2 retrocopies	retro_rnor_2671, retro_rnor_2729,
Tursiops truncatus	ENSTTRG00000002654	2 retrocopies	retro_ttru_1566, retro_ttru_1890,