RetrogeneDB ID: retro_pabe_952

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:97564236..97564530(-)
• Located in intron of: ENSPPYG00000004853

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_952
GAAATGATTCATGAAGCTGTAACCTTGAATTGGAAAGTGGAACACAGGTCTATGGAACAGTCACAGGTGTGGATGTCACC
GTGATACACATCTTAAAGCATGAAAATGACCCTGAAGACAGAGAACTTGTACAGTTGGAAACACAAATTTGAGGAAGTAA
CATTAGATATTTTACTCTACCAGACAGTTTACCTCTGGATACACTACTTGTGGATGTTGAGCCTAAGGTAAAAACCTAAG
AAAAGGGAAGCTGTTTGTTGCAGGAAGAGGCCAATGCAGAAGAAGAGGTAGAGG

Alignment

ORF - retro_pabe_952 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 84.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KLSHETVTI-ELKNGTQVHGTITGVDVSM-NTHLKA-VKMTLK-NREPVQLETLSIRGNNIRYFILPDSL
          ...HE.VT..EL..GTQV.GT.TGVDV....THLKA..KMTLK..RE.VQLET..I.G.NIRYF.LPDSL
Retrocopy EMIHEAVTL<ELESGTQVYGTVTGVDVTV<DTHLKA<MKMTLK<DRELVQLET-QI*GSNIRYFTLPDSL

Parental  PLDTLLVDVEPKVKS-KKREAVAGRGRGRGRGRGR
          PLDTLLVDVEPKVK..KKREAV..R.R.....R.R
Retrocopy PLDTLLVDVEPKVKT>KKREAVCCRKRPMQKKR*R

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	19.02 RPM
SRP007412_cerebellum	0.12 RPM	23.71 RPM
SRP007412_heart	0.12 RPM	8.01 RPM
SRP007412_kidney	0.03 RPM	14.78 RPM
SRP007412_liver	0.03 RPM	10.74 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_952 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_952 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_952 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1147
Pan troglodytes	retro_ptro_781
Macaca mulatta	retro_mmul_891

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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,