RetrogeneDB ID: retro_pabe_380

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:45073143..45073498(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPCS1
• Ensembl ID: ENSPPYG00000013798
• Aliases: None
• Description: Signal peptidase complex subunit 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5RF96]

Sequence

>retro_pabe_380
CCCTCACCATGCTGCCCACTGCCTGCGCTCCACCACCTGCCTCCGTGGCCAGTCATGTTGGAGCATATGAGCTTGCTACC
CATACGAATAGATTACAAGGGACAAAAGCTAGTTGAACAAATGTTTCAGAGAATTATTATTTTTTCTTCAGTCATTGGAT
TTATCTACGGTTATGTGGCTGAACATTGCAGATGAACTGTCTATATAGTTATAGCTGGATTTGCTTTTTCACATTTGCTG
ACACTTCACCTGTGGCCCATCCATCAGTGGCATCCCCTCAAGAGGTTACTTGTCCAAGACTCATCACAAAAAATGAGAAG
CTGGGGATAGAAAAATTAAGAGGCACGCTAAAAAT

Alignment

ORF - retro_pabe_380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.12 %
• Parental protein coverage: 70.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PSPRSLPPALSCPPPQPAMLEHLSSLPTQMDYKGQKLAEQMFQGIILFSAIVGFIYGYVAEQFGWTVYIV
          PSP....PAL...PP.P.MLEH.S.LP...DYKGQKL.EQMFQ.II.FS...GFIYGYVAE....TVYIV
Retrocopy PSPCCPLPALHHLPPWPVMLEHMSLLPIRIDYKGQKLVEQMFQRIIIFSSVIGFIYGYVAEHCR*TVYIV

Parental  MAGFAFSCLLTLPPWPIYRRHPLKWLPVQESS-TDDKK-PGERKIKRHAKN
          .AGFAFS.LLTL..WPI...HPLK.L.VQ.SS.T...K..G.RKIKRHAKN
Retrocopy IAGFAFSHLLTLHLWPIHQWHPLKRLLVQDSS<TKNEK<AGDRKIKRHAKN

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	24.88 RPM
SRP007412_cerebellum	0.00 RPM	25.54 RPM
SRP007412_heart	0.00 RPM	12.10 RPM
SRP007412_kidney	0.03 RPM	33.91 RPM
SRP007412_liver	0.03 RPM	28.25 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_380 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_380 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_294
Pan troglodytes	retro_ptro_241
Gorilla gorilla	retro_ggor_332
Macaca mulatta	retro_mmul_549

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008426	1 retrocopy	retro_amel_1899,
Canis familiaris	ENSCAFG00000008927	1 retrocopy	retro_cfam_2079,
Equus caballus	ENSECAG00000023559	1 retrocopy	retro_ecab_86,
Erinaceus europaeus	ENSEEUG00000007914	1 retrocopy	retro_eeur_25,
Homo sapiens	ENSG00000114902	1 retrocopy	retro_hsap_294,
Gorilla gorilla	ENSGGOG00000028027	1 retrocopy	retro_ggor_332,
Microcebus murinus	ENSMICG00000014061	1 retrocopy	retro_mmur_292,
Myotis lucifugus	ENSMLUG00000000744	1 retrocopy	retro_mluc_2104,
Macaca mulatta	ENSMMUG00000017370	1 retrocopy	retro_mmul_549,
Otolemur garnettii	ENSOGAG00000004106	3 retrocopies	retro_ogar_2119, retro_ogar_2315, retro_ogar_2788,
Pongo abelii	ENSPPYG00000013798	1 retrocopy	retro_pabe_380 ,
Pan troglodytes	ENSPTRG00000015011	1 retrocopy	retro_ptro_241,
Tarsius syrichta	ENSTSYG00000006854	2 retrocopies	retro_tsyr_1359, retro_tsyr_599,
Tursiops truncatus	ENSTTRG00000008576	1 retrocopy	retro_ttru_806,
Vicugna pacos	ENSVPAG00000007380	1 retrocopy	retro_vpac_269,